Isn't it so that even when you're rolling around in your UFO, you can take a step back, park the saucer, and check out your citizens? I mean, from what I gathered one can still very much go to the Civ-level, the UFO is mostly just a way of transport, and for general messing about.
I really don't see how it would be possible to have more than one UFO, because really, you can't control one around. You ARE one, when you have the UFO-mode turned on. When you don't, you're at Civ-level. One would need a completely different interface in order to order UFOs around, because you can only assign two out of three coordinates at a time. So, I think I can nearly guarantee there will only be one UFO. Not to say you can't have a thousand UFO-designs, and pick and choose between them as you like (dunno how that might work).