There are several great videos available in how to properly replace a skylight. I like this one:
http://www.surebond.com/rvautomotive.html
Be sure and use your sealant sb140 or dicor both underneath the skylight edge and over it. The method in the video worked well for me on my rubber roof.
The last several I replaced I did use a thick bead of dicor underneath. Make sure it squishes up through all the screw holes and around the edge. I then used eternabond all around, and used dicor on all edges of the eternabond. Be sure and do not over tighten the screws. Have had good success so far.
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Scott and Liz - Southern NM
2012 Wildcat Sterling 32RL - w/level up (best option ever)
2007 Chevy 2500HD Duramax
Reese Fifth Airborne Sidewinder