I'm no expert, but here's what I did on my ES.  I followed the logic for the dual electric system set out by Bob Nuckolls at Aeroelectric.com and on the Aeroelectric List.  The model is Figure Z-14 at Aeroelectric.com, modified to allow for rear batteries.  Both batteries are located on the bulkhead in the back of the baggage compartment.    My wire bundle from the back runs along the right side of the fuselage through each bulkhead.  This bundle includes three fat wires, comprised of two battery positives and a single ground wire that ties together rear and forward ground buses.  I don't plan a FADEC system, so the redundancy of having two grounds cited by John Schroeder was not an issue for me.  The bundle also includes smaller wires for forward components driven off the battery buses (overhead/baggage lights, clock, elt, hobbs, aux fuel pump) and the contactors, which are located  near the batteries.  The components run off the battery buses are fused using inexpensive fuseblocks supplied by B&C.  Components driven off the primary and auxiliary buses in front have breakers (just my preference).  I do not have an avionics bus.  Some think that's nuts, but I am convinced it is not necessary and adds unneeded complexity.  I pulled all the wires from the rear together in a single bundle and fastened the bundle to the fuselage side with Adel clamps mounted to studs floxed into small pieces of phenolic floxed to the fuselage side.  There is one hole through each bulkhead, big enough for this bundle.  My antenna wires run down the other side of the fuselage in a similar way.  Unlike John Schroeder, I did not separate trim and signal wiring from the rest.  We'll see if this creates any noise issues.  I think I also ran strobe wires down the left side, because I mounted my strobe pack on that side and it was convenient to do it that way.  We'll see if this raises noise issues.  This can be changed if necessary at relatively low cost.

I recommend visiting Aeroelectric.com, purchasing Nuckolls' book, and joining and reading the Aeroelectic List.  I learned more about aircraft electrical systems from these sources than reading anything else.