you have to manually follow a supply ship. This is a real pain in the a**.... if only our fighters had "track" buttons like UFO did.
since they don't, you can just right-click and follow a supply ship around till it vanishes... pause the game, zoom in to where it vanished, and right click there. If you're right on top of it, your ship will scout the base.
I spent quite a while playing before I realized I probably had no bases, because I was shooting everything down.
I let them land once or twice, and then there was a base...