I would mount the solenoid at the batteries so that you are minimizing the number of long lengths of positive wire. Then you just have one short wire that connects the two batteries via a solenoid and one long wire that runs up to the front of the truck to power your stuff. You can power the solenoid off of the reserve battery and then run a small fused wire to a switch in the cab and/or your ignition.

In terms of the ground, I would ground the batteries in several places just to be safe. Ground at the frame near the batteries and also run another wire up the front to ground there and on the engine block. If you are using the batteries to power your ignition, you can then be sure you have good current.

Running long positive wires under your chassis is very dangerous. One thing I did to help minimize any shorting out problems, which can lead to fire, is run the wire through heater hose. The Heater hose is big enough to accept pretty large wire and will give pretty significant protection to the wire.

You should also consider running a fusable link at the batteries for ulimate protection. Wrangler NW sells 200 amp continous fusable links, which would be enough for anything except maybe winching.

Hope I didn't just repeat what everyone else said, I didn't have time to read the entire thread.

Good luck.