Check out
This Link for a lot of useful information from Googlie about scenario creation. Much of the basic material is covered in an easy-to-follow fashion.
Regarding your specific question (disclaimer, I am not an expert at this), if I understand it correctly, you may need to "select the faction" first, then place the units. I don't offhand remember the keystrokes and/or menu steps, but that is an important step, or else your units will belong to whatever the "current" faction is. There may also be preliminary steps/selections necessary to get to the point where you are placing units - perhaps you need to specify that you want to work with "all factions" instead of just one at some point. Various other characteristics such as morale can be set for each unit as well. False starts (like placing the units from another faction in the wrong territory) will have unpleasant side effects when playing the resulting game - in that case, even if you delete the units, the tiles they occupied will be visible to their faction as if they had been explored. The Scenario Editor is not perfect, nor is it particularly intuitive, so being careful and saving are worth while in this process. OTOH, some of its idiosyncracies are fun, like its ability to put sensor arrays in the ocean.
IIRC, if what you want is to create a base, you have to start with a CP, and then start the base as in the game with the Build command.