I rate the Gore Professional cable kits highly - spendy but fully sealed and work exceptionally well when installed correctly. Very slick feel at the lever when shifting.
There are supplementary cable guides you can get - such as the ones from Problem Solvers:
http://problemsolversbike.com/products/hydraulic_brake_hose_guides/This will allow you to run full housing. Just remember to run SRAM inner cables with SRAM outer casing, or Shimano with Shimano as the inners and outers are different diameters between the brands, as well as the genuine lube for both.
OK, official shop mechanics hat off, you should run matched branded cables together (due to sizing differences) but will still work if you mix and match, YMMV. Slick Honey or similar thin silicone lubes work well too.
Witha frame bag, just run the straps under the exposed cable inners.
