I was in the same boat when we bought our first fifth wheel. My thread here was titled something like "minor leak question". It turned out to be a big project involving rot repair and several leak points.
Whatever you do, don't just caulk or tape over something. Remove the window or trim seal piece and install new putty or butyl tape under it. Then caulk if need be. Don't use DAP or other residential grade caulks. The generic recommendation is Dicor Lap Sealant on the roof, and Proflex RV caulk on the vertical surfaces. You can't go wrong with those. Of course there are equivalents.
There are plenty of videos of youtube on how to remove a window, or trim, etc. Neither is as scary as it seems. Windows are a piece of cake. Trim can be more involved, but it has to come off if it is leaking, unless you Eternabond over it. With as much rot as you've found, I'd say take the thing apart and fix it. Sorry. Or, sell it now. Actually, that's the best course of action, speaking from experience.
Take a look at the rotdoctor.com website. You may or may not be able to make use of his stuff at some point. I can attest that it is good stuff. And it does require a fumes respirator.