Others that know more should reply soon, but I've used silicone on sides so far. Dicor self leveling on any roof areas. They make a no-sag caulk too I believe. That may be a better choice on sidewalls. The best thing to do, whatever you use, is to make sure you prep well first. Scrape and/or cut out three old caulk first, and then clean the area before re-caulking.
Again, I'm no expert, but this works for me
Joel and Teresa
2016 Sabre 34TBOK
2006 GMC 3500 CC LB DRW 4X4