What material is your roof made with? Is it fiberglass, rubber, (there are 2 main different types of rubber roofs), or something else.
If it's a rubber roof, you want to use Dicor Lap Sealant. Silicon sealers will eat the rubber on a rubber roof and eventually cause even more serious issues within a short while. Silicon does not hold up very well against the elements either for around windows and the running lights on any camper. For sealing anything on the side of your camper, no matter what the skin is made with, use Butyl putty. It comes in a roll and is applied before installing the item on the camper, like a gasket.
If your roof is fiberglass, you'll probably want to reseal those holes with an fiberglass epoxy sealer.
If it's metal, something like Eternabond tape is a good choice. Actually, Eternabond is a good choice for all surfaces to cover a rip, a tear, or a hole.