There may be many more questions that you have about specific issues you could have while creating your mission.  Here are a few questions and answers that may help you.  Another resource is the Mission Authoring group on the Warfare Incorporated Forum.  They are organized loosly by topic, but read through them all to get some clarifications, and some good ideas.
How do I make an Ecom? Ecoms are very simple. Just create a trigger with the conditions you want, and as an action select "Ecom". It will ask you several things, like the size of it, if it goes on to another ecom or just closes, and the people involved in it. Fill all these in, and you're done!  Remember that Ecoms are only used in single player missions.
Why do weird things happen when I put an @ in an ecom?
If you've ever put an @ in an ecom, it will make a new line and pause the game for a few milliseconds.  Here is what you do if something weird happens with it.
The @ sign was an escape code for the developers of WI. Nobody knows why it makes a new line, but if you put two of them next to eachother, it will come out as a regular @ with no problems.
How are countdown timers set? 
Countdown timers involve two Actions: Start Countdown Timer, and Modify Countdown Timer.
  1. To start a countdown timer, first create a new trigger. 
  2. Select any players and conditions you want. 
  3. Select the action Start Countdown Timer.  Enter the # of seconds, and then the name.  The name looks like this: "%s Until Wave Arrives". The %s is the time. It must be in this format.
  4. Create action Modify Countdown Timer and set it to show it.
Ok, we have our countdown timer, and its ticking, now what? Well, we somehow have to turn it off when it reaches zero. For this, after the action you just made, we put a wait in.
  1. How much was the countdown timer set for? Five minutes? Then we will wait 300 seconds. Or however long the countdown timer was set.
  2. Now, another action: Modify Countdown Timer. And just tell it to hide the countdown timer. You're done!
How can I create a death trigger?
Death triggers are triggers that happen when something dies. Like Andy, for example. You want the game to end when Andy dies. You'll need a trigger like this:
    Condition 1: Side1 commands exactly 0 Andy.
        Action 1: End mission with defeat.
How do I string levels together in a campaign?
If your mission is part of a campaign (like the story missions in the game), you can have the game load the next mission in the campaign automatically when the current mission ends. You do this by including a Set Next Mission Action in your mission. If you want the game to load a different next mission depending on how the current mission ends, you should include the Set Next Mission Trigger Action in the trigger that has the "End Mission" Action.
The name you use with "Set next mission to" is the title you have set in the LevelDoc settings for the next mission (Settings -> Level -> Title) followed by ".lvl". The TriggerAction should look like this:
Set next mission to "My Next Mission.lvl"
NOTE:  "The "Set Next Mission" mission name is the first 22 characters of the mission to be linked to, followed by ".lvl". If your mission is less than 22 characters, it is the full name of the mission followed by ".lvl"."
How can I make the enemy attack?
You create a unit group with all the units you want. 
At the top of the Unit Group window there is a drop down menu for Aggressiveness.  Select Pitbull.  This will cause the units in this group to go in search of an enemy to destroy.
Another option, if the user wants the unit(s) to seek out and kill enemies, is to use the Unit Action "Hunt Enemies".  When you place a unit, the properties will be on the right in M. There is a property called Action. If you click on the ..., you can set the Unit Action to execute for that unit. The first 3 settings are related to guarding, and one is "Hunt Enemies".
Can they attack in waves?
Sometimes people want an enemy to attack every 5 minutes or so. In this case they would make this trigger:
    Condition 1: Every 300 Seconds (300 seconds = 5 minutes)
        Action 1: Create Unit group "Attacker"
        Action 2: Preserve Trigger
Another way to do it would be this trigger:
    Condition 1: Always
        Action 1: Create Unit group "Attacker"
        Action 2: Wait 300 seconds
        Action 3: Preserve Trigger
Or if you want to make them attack in waves that continually get stronger, just make this kind of trigger:
    Condition 1: Elapsed time is 600 seconds (10 minutes)
        Action 1: Create Unit group "Attacker 1" (Which consists of weak units)
How can I make units guard areas?
Make a unit group with the unit you want, and set it to guard right after it appears.  When you place a unit, the properties will be on the right in M. There is a property called Action. If you click on the ..., you can set the Unit Action to execute for that unit. The first 3 settings are related to guarding.
Is there a way to put structures into a unit group?
Yes in fact there is, but the editor wasn't intended to do this, so use this at your own risk.
  1. First select any trigger and add an action to it called create units at location and create whatever building you want, at any location (it won't matter).
  2. Now try saving and compiling (you don't have to play it).
  3. When you re-open the editor, go to the unit groups and hopefully somewhere in there will be a cauu# group, with a structure in it.
  4. Rename it to something else if you want.
  5. Go back to the action you created and delete it.
  6. Repeat the process any amount of times.
NOTE: This may not work in some versions of the editor. 
What are persistent variables?
Persistant variables, or pvars, are variables that can store numbers.
Use the Modify persistant variable action to "Set" or create them for the first time. After that, use modify to add to, subtract from or set to a value. To use in a trigger, Test the pvar for the value, or range of value. For example, if you want to have an action happen after the player has been through an area X times:
    CONDITONS:  Mission Loaded
        ACTIONS:  Comment: Create pvar myCount
                        Modify persistent variable 'myCount': Set 0
    CONDITIONS: Comment: Check area XING for Player
                        Area 'XING' contains AtLeast 1 AnyUnit owned by side1
        ACTIONS: Comment: Increment myCount
                        Modify persistent variable 'myCount': Add 1
                        Preserve Trigger
    CONDITIONS: Comment: See if player has been to XING ten times
                        Persistent variable 'myCount' is AtLeast 10
        ACTIONS: Create Unit Group 'AttackForce'
You could reset myCount to zero at this point, and add a Preserve Trigger to the above. Then every ten times (or whatever number you want) the trigger would activate.
Another example:  Using Pvar as a counter...
    CONDITIONS: -Comment: Game Seconds
                        -Every 1 seconds
        ACTIONS: -Modify persistant variable 'GS': Add 1
                        -Preserve trigger
    CONDITIONS:  -Comment: Game Minutes
                        -Persistant variable 'GS' is Exactly 59
        ACTIONS: -Modify persistant variable 'GS': Subtract 59
                        -Modify persistant variable 'GM': Add 1
                        -Preserve trigger
    CONDITIONS:  -Comment: Game Hours
                        -Persistant variable 'GM' is Exactly 59
        ACTIONS: -Modify persistant variable 'GM': Subtract 59
                        -Modify persistant variable 'GH': Add 1
                        -Preserve trigger
Is it possible to locate a specific unit and have the focus center over it? 
As for locating a unit, that is very intensive. Basically, you create an X-Y grid of overlapping areas. You must then test each area for the unit, and then modify a pvar to keep track. You can then cause the game to recenter over the unit.
How do I make a bullpup mine?
There is a really easy way to do this. Select the bullpup(s) you want to have mine, and in their properties, set their behavior to "mine".
How do I copy and paste?
When you want to copy a unit, hold the mouse over that until and hold down control, and drag the unit somewhere. There's your copy!
Is there a limit on switches?
Yes, you can have a maximum of 16 switches.
Is there a limit on triggers?
Although the editor doesn't stop you when you go over, the limit is 40 triggers per side. If you go over this, then it won't work.
Is there a limit on areas?
Yes, the limit is 32 areas.
What's the difference between the difficulties?
You can test difficulty in a mission to trigger actions to make it easier and/or harder. BUT even if you don't do this, the player's difficulty choice influences a few factors of the game. Here's how it works:
- no special advantages or disadvantages (this was the internal default setting for most of the development of WI)
Normal bonuses
- decreased build time for player structures
- increased armor for player structures & units
- player can see if enemy is low on power or credits
Easy bonuses
- all Normal bonuses
- increased player unit firepower
- increased value for player's Bullpup Galaxite deliveries
The design concept for the easier difficulty settings was to crudely simulate the advantages that more skilled players have to give less skilled players a boost in ways that wouldn't throw the missions out of wack.