A picture would help us to understand the first part about the sealant between the slide and trailer.
As for roof maintenance, here are some of my thoughts.
Its a requirement that you maintain the roof for warranty purposes. More importantly, this little piece of maintenance will save you lots of money and possible heartache down the road.
INSPECT: Do this every few months. Get a tall ladder and climb up on roof (It will support your weight). Use a board if you want to (I don't) and step clear of A/C, vents, skylight, etc. Inspect all seams, gaskets, and any place that the roof material has been cut or drilled. Check closely around A/C, vents, antennas, sewer vent, every screw, and all side seams. You are looking for dry or cracked caulking. Also, look for any signs of bubbling in the membrane and any tears (damage from tree branches, etc).
CAULKING: Do NOT use silicone. I use Dicor 501 Self Leveling for sealing cracks in the existing caulk. Take your tube of Dicor and a caulking gun and simply squirt a dab of the Dicor on anything that looks like a hole or crack. You shouldn't have to remove the old caulk unless something is really wrong with it.
As for cleaning the roof... I am not positive if you have an EPDM or TPO roof. Check the paperwork you got with the trailer. I use Murphy's oil soap to clean my TPO roof. Whatever you have, you want to stay away from anything with petroleum in it. Here's a helpful primer on cleaning an EPDM roof Cleaning the Rubber Roof
Hope this helps!