One thing to note:
If you change the positions on the map by deleting the existing ones, and placing them elsewhere, be sure to go into the reveal tile mode and clear for all civs. It is an easily overlooked step.
Also, I noticed that when moving, you can't specify the starting units the way they are in the game. In other words, if you examine the units, you will notice that most are colonists with designations as soldier or pioneer. You can't change that when adding specific colonists and you must put in Hardy Pioneer and Veteran Soldiers from the get go. Not too big a deal, but you just can't get them exactly as the game defines (unless you go in and edit the xml, probably)!