You can join your cables with techflex, or just a tiny strip of gaff every 18" or so, depending on how long your cables are. Even when the cables are taped together, you can still neatly coil them up (oevr/under) and store them in your bag in front of your recording deck. Better yet, chop your cables down to a length that is suitable for most open taping situations, and use the remaining cables to make extensions for when you need a little extra length.
The pins for active cables are usually small and delicate, I think the best way to protect these is to usually leave them always plugged in if possible. Constant plugging/unplugging will wear out your connectors quickly, so leave them plugged into your mics/pre/deck when you can. This is more important when you're dealing with proprietary connectors (microdot, dpa, schopes kc5, etc) when replacing the cables is prohibitively expensive or impractical.