Time spent planning your mission ahead of time is always time well spent. Be as organized as possible and write down your ideas. Here is a basic checklist for planning a mission. The more planning you do before diving into the Editor, the easier it will be to create a successful mission that everyone will enjoy playing.
First, Single player or Multi-player?
Must I start from scratch?
NO! The Mission Editor has the ability to import existing .pdb files so that you can modify and save them as a new mission. You can go to the Forum and tap Download on any of the mission .pdb files. Save them in your M folder, or wherever you will remember. In the Mission Editor go to File / Import Mission Pack. Navigate to the .pdb file you have just saved and click Open. Then be sure to save it as an .ld file. You can check out all the triggers, unit groups, etc. that have already been created. Modify the mission in any creative way you want to, and save it as a new mission.
NOTE: Switches and Areas are named. Be sure that you give unique names to all your switches, areas, groups, variables. This is very important as the Editor will not warn you if you have duplicates.
Also... if you delete or rename an Area or Switch you will not be warned. It just won't work. So be sure to watch out for these changes.
Now open M (the editor) and start implementing your ideas.