I carry two kayaks in my bed all the time (both 12 ft. long). I have the CC SB just like you and it works fine. Granted I don't drive very far, maybe 15 miles one way, but it works fine. If I go on the longer trips I'll just throw them on top of my OEM Utili-track Roof Rack.
I don't have a tonneau cover like yourself, so I couldn't help you out on any advise there.
Good luck to whatever you decide to do. Be sure to let us know.

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2006 Granite Crew Cab SE 4x4 w/ Big Tow
285/70/17 BFGoodrich All-Terrain T/A KO
DIY Air Box Mod w/ Drop in AMSOIL EaA Air Filter
Sway-A-Way Coilovers w/ PRG UCA and Sway-A-Way w/ Reservoir Rears
TomTom One XL Navigation
AMSOIL Signature Series 0W-30, 75W-140 Severe Gear and 75W-90 Severe Gear
Magnaflow 18" muffler swap (PN: 12256)
2* Timing Advance
PRG Shackles (
Still need to install these...)