Silicone caulk works well on vertical surfaces due to its ability to stretch with expansion, contraction, and vibrations. But I prefer to use the Dicor non-sag caulk for fiberglass seams. It, too has the ability to stretch and endure vibrations, but adheres much better over time. And I believe that's what a dealer would recommend, for warranty purposes.
I use the Dicor self-leveling caulk on the roof seams, and the Dicor non-sag on vertcal seams. But I also use the clear silicone around marker lights and utility openings, like water hookup doors, etc.
2015 Jay Flight 32RLDS Elite
2012 Chevy 2500HD Crew Cab LTZ (6.6L Duramax/Allison)
Equalizer Hitch (1200# bars)