Control selecting multiple bases can't work until after the bases have been built.  At that point I don't need any help figuring out where the next base goes; but at that point if the location I need is blocked by terrain it's already too late unless I want to destroy existing bases to adjust the layout.  It's figuring out where the first one needs to go so the layout doesn't end up blocking on one of the followup bases that's the problem.

I have done two things.  First, a constructor has a marked ring around it as it flies. so I move a constructor around and see where it covers.  In one crowded situation I had three constructors in the area looking for how they could cover everything.  It was an interesting little puzzle.  Second, I have drawn out the the pentagon pattern that surrounds a single planet on hex paper a few times to get a feel for it.  I can now pretty confidently count out and "see" the pattern on the map.  I have done the same for a few other key starbase patterns.  It helps an awful lot in being able to visualize the patterns fitting onto the map.

All in all, it gets better with practice.