I know that this is an old post, but it's the only one I found when searching for "choose where the enemy starts".
I also know that GoogleFrog of course knows this (thanks, by the way), but it might be useful for other players.
So, this is how to choose where the enemy starts and where we start, in a single player skirmish.
I put dots to indent the lines, because I don't know a better way.
________________________________________Before starting the match, click:
..Advanced
....Options
......Start (it's a tab in this small window)
........(On the left of "Start boxes", click the drop-down menu)
........Start anywhere
........(Check the box on the right of "Set AI spawns")
Then click "Apply".
Then start the match by clicking "Start".
In the upper left corner there will be a box named:
..Set AI start positions
Click on a listed player.
..Click on the map, where you want him to start.
Repeat this for all the enemy players.
Click on the desired chassis for yourself.
..Click on the map, where you want you to start.