The monocrystalline panels will give you a higher output. It really depends on the quality of the panel - high end polycrystalline panels can get close to low end mono panels, but in general, you might expect 10-20% more output from the mono panels.
For a home, its sometimes cheaper to go with more poly panels. On an RV, where space and weight are issues, the mono crystalline panels probably make more sense.
You can also check out www.solarblvd.com
for panels or complete packages. And if you buy there, find them on e-Bay. Sometimes they sell the same item for less on their e-Bay store. For best price, poly panels from WindyNation seem to be one of the best deals out there.
As for the roof warranty - its the same idea as adding vent covers - if there is damage or leaking related to something you installed in the roof, its not covered by warranty. If something totally un-related goes wrong with the roof, then it would still be covered.