You have two ways you can go about this.
1. Create the mission in Zeus in game, save it using one of the Ares modules, and load it later when you want to use it. You can pick right up where you left off.
2. Delve into the mission editor as CPL Bingham suggested. To answer your question, yes it would effect ACE medical and the like if you didn't include the right modules and files in the mission folder. A good place to start is to just take one of the unit's templates and edit from there. That way you have all of the modules, player slots, and files and can just start placing enemies down. SSG Ryan is kind enough to include the source mission folders in his
mission file thread here. You can grab the template for what map you want and start editing it.