How do you get the old caulk off? What brand of caulk do you use on the sides around the lights and windows?
How do you get the caulk off is the first and foremost question needing a good answer. Then of course, what brand do you use to replace the old is a must have.
The roof is easy, Hot soapy water with a soft brush to clean and Dicor self leveling caulk as the sealant. If it is really thick or been patched a couple of time use a plastic scraper to remove the bulk but do not attempt to get it down all the way to the rubber roof.
The side lights are a different matter. Silicone caulk was used and it is a bugger to remove or even clean up. For these locations I prefer to use a 100% latex Caulk but it will require regular attention. If you just want to patch a thin spot on the existing caulk you can clean it again with hot soapy water and then use a thin spread of 100% clear silicone caulk.
The Windows and doors are sealed with Butyl tape and should not be caulked. If they are leaking the window or door should be removed and the old Butyl removed and a fresh seam laid down and the door or window re installed.