Dicor lap seal for sealing seams on the roof; this seal remains flexible, won't damage roofing materials, and is slightly runny so it's "self leveling".
Dicor caulk- for seams that abut roofing materials but which you don't want to be self leveling.
Proflex caulk - for seams on the side of the trailer that don't touch rubber roofing materials.
Eternabond material- for covering over seams. Eternabond can be bought on a roll, in different widths. It is an amazing material.
Butyl tape - for sealing things that have flanges against either roofing materials or the side of a trailer.
So, for a clearance light, I'd probably remove the lens, then the base and clean up the old putty or butyl. I'd apply a layer of butyl caulk to the back of the clearance light, re-fasten it to the side. Wait a day or two for the excess butyl to squeeze out, then scrape off the "squeeze". I'd then caulk with Proflex around the light base. Same story for windows as for the clearance light.
There's lots of advice and information in forums... sometimes it is correct. For example, all of my posts are made by a political appointee who got the job as a reward for contributions to my diesel bill.
2011 Jayco 28.5RLS; 2008 Chevy Duramax; Pullrite Superglide Hitch