I looked through search briefly, but wasn't able to find anything quite addressing the same issue. Basically, in system manager, the only template which i can successfully place as a moon of another planet is the moon template itself. Other planets are acting oddly, sometimes they'll snap to a nearby planet, most of the time they wont. It's hard to build maps like this, because pretty much none of my planets can be in orbital relationship of each other, taking interplanetary nukes off the table.
...Unrealistically. Then again, if we are being realistic, we might as well go hardcore or not at all. Orbiting wouldn't allow moons in moons in moons, and those are fun, so let's allow big to orbit small if we so desire.