I loaded a test map back into the editor and the built bases exploded. The other build pads version are for capture, and I think are blank for use in GC mode where you buy your buildings and then they show up on the planet in those designated spots.
Skirmish mode maps are easier to make. There are different types of the same building, depending upon what they are used for Skirmish, Capturable freebee, Galactic Planet Mode, Skirmish Mode where you must build up your base first. Even Neutral.