Mike,
Played around a bit last night. This diagram assumes the VFR airplane is already wired conventionally, and the goal is to add a backup battery system dedicated solely to keeping an EFI/EI working if the primary electrical system goes down...due to failure, or because the pilot found it necessary to kill the master.
It is also simple, requiring little in terms of special knowledge to fly it safely. It's got a master switch; on or off has nothing to do with keeping the engine running, just like a magneto airplane. It's got one or two ignition switches, depending on single (left diagram) or dual EFI/EI controllers (right diagram). It's got a fuel pump switch, which the pilot must turn on or the engine won't start. The pump switch only allows running one pump at a time, important with EFI. A pump failure requires a switch action from the pilot, but any current EFIS/EIS takes care of problem identification. The pilot gets a low fuel pressure warning, and reaches for a pump switch, again very conventional. BTW, that too can be made automatic.
I've drawn in fusible links for the EFI/EI battery feeds, bulletproof when fabricated properly.
The two batteries are isolated, so a lithium aux battery is possible, assuming the answers to other issues are positive.
One of these might work well to feed the single EFI bus:
http://www.periheliondesign.com/powerschottkydiodesfiles/Power_Deuce_Schottky_ Manual.pdf