First, (and I know a lot of trailer and RV manufacturers use Silicone sealants because they're cheaper than quality sealants,) I hate them, and avoid them like the plague. Once applied, you will not have a good seal after a couple of years, and nothing else will stick where it was used, ironically, not even more Silicon sealant. My preferred sealants are 3M 4200 or Sika-Flex.
And I would also recommend removing the window and applying the sealant between the window and the trailer shell. Just squeezing a bead of any sealant around the outer edges is a disaster waiting to happen.
For mounting
windows, my choice is Butyl Rubber weather stripping, (available at any auto parts store.