The pad you'll use depends on which wheels you buy. Enve and Reynolds specifically say not to use cork pads on their wheels because the cork pads cause heat issues, which causes failure issues, which can cause death issues. Both companies have their own pads, which they require you to use if you want to be able to claim a warranty issue. That said, either company's wheels work quite nicely with SwissStop yellow pads, and you're going to have to do some reaaaalllly dumb stuff to heat fail a carbon rim in the midwest, so I wouldn't hesitate to run SwissStops if I needed to.
Most of the other stuff out there ships with a set of cork pads or recommends cork. I ran cork pads on my old Bontragers and cooked a set of pads in like 6 weeks. After that, I switched to SwissStop, which also wear quickly compared to rubber pads on aluminum rims, but at least make it through a season.
I have run SwissStop yellows on both aluminum and carbon wheels. They're good on carbon, and they're "there" on aluminum. It's not scary, but it's not as good as pads designed specifically for aluminum. I have also run Reynolds CryoBlue pads on carbon and aluminum rims, again with the same results. If you go with the one set of pads strategy, check the pads when you switch wheels to make sure nothing's stuck in them. If you go with the two sets of pads strategy, check the pads when you put on the carbon wheels to make sure nothing's stuck in them. Why bother if you have carbon-specifice pads? Because two minutes (if that) to pick a pick of crud out of a pad is well worth saving yourself the brain damage of realizing you've gouged a fancy rim, or worse yet gouged a fancy rim and caused it to heat fail because you wore through the layer specifically designed to deal with heat (applies mainly to older Reynolds and Edge/Enve stuff).
Let me know if you've got more questions I can help with.
Shameless plug: Buy my Reynolds SixtySix set that I have for sale in the classifieds!