If you have insulation between you and a vapor barrier like mylar, the insulation will likely get wet from perspiration.
Pads generally have a higher R-value per thickness than underquilts, so you might get to 30F with 1" of CCF pad, whereas you'll need 2" of uncompressed down under you for the same temp. But the down will compress much smaller in your pack and cover much more area of the hammock than a pad will. If you use a pad in a hammock, you'll need to consider how the pad wraps around your hips and shoulders...use a SPE or something. Keeping a pad will enable you to go to ground if you want to, as well.
Heat rises, but most hammock users report being colder on bottom than on top, due mostly to convection (wind blowing under you). I've been sweating on top and freezing on bottom before. So I'd use the same thickness below. If I had two different thicknesses, I'd choose the thicker one for the bottom. Just me, though.
You might check BGT to see if users have reported a difference in warmth with the SuperShelter when using quilts vs bags inside.
Underquilts can be more succeptible to getting rained on simply because they're outside the hammock. Using a tarp that provides adequate coverage solves the problem easily, though. I've found the stock HH fly too small (other folks don't have a problem with it). I'm comfortable with the JRB 8x8...it's plenty big enough for my UL BP Asym and very light for the coverage you get. The MacCat gives better protection on the ends (where I've experienced the only problems with wind-blown rain) and more useful area along the sides due to its shape, but weighs just a bit more and you need 4 stakes w/ cords. Both tarps have die-hard fans, and both are quality pieces of gear. MacCat is coming out with a Micro model...I'll be interested to see how it compares with the JRB.
Lots of rambling...hope it helps!