Congratulations on your new boat!
First, avoid using silicone on a boat at almost any cost. It leaves behind a nasty residue that's almost impossible to remove and that future paints or sealants will never stick to. The only way to get rid of it is to sand it away - which you don't really want to be doing to gelcoat if you don't need to. Save that stuff for your bathtub at home.
I don't really know of any quick fixes for your situation that won't ultimately make it harder to do the job right when you're ready. I think if it were me I'd just make sure the water wasn't getting to the headliner, interior woodwork, or upholstery and just live with it until I could fix it. If you're not going to be using your boat much over the winter you can always make a boom tent with a plastic tarp to keep most of the water away.