RTT mounting position....

OK, so I ordered my first Tacoma (traded in my '06 4-Runner) and I'm probably going to get in on the Cascadia group buy this spring but now I'm curious about mounting locations and options. Initially I was planning on purchasing an ARE cap and putting a rail and rack system on top of it for the tent but I called the dealer back and told them to also install the roof rack on the truck's cab. It's a 4X4 DCLB for what it's worth.

In addition to the RTT, I would also occasionally haul kayaks with the truck (maybe with the tent and maybe without) and would like to have the option of using a rack system even if I had removed the cap for whatever reason. Would anyone like to give some pluses or minuses with the mounting position, either on the cab rack or on a cap? Personally, I think the caps look much cleaner without any rack on them and for this reason I'm leaning towards mounting the RTT and kayak racks (when used separately) on the Toyota rack on the cab of the truck.