Ryan and Vin:
Currently, all my birds , including my F-100D, F-4, Firebird, and KC all use the same setup. Dual A-123 and Andy Lo's(ElectroDynamics) Battery Backer(EDR-108T) with two leads input and 2 leads output. He rates at 6 amps continuous and 20 amps pulsed at a 20ms On/40 ms Off cycle. I use JR 1222 with EC-3 connectors and integral soft switch. Andy's unit is so small with no bulky external heat sink that you can hide anywhere with sticky tape.
I have Andy wire everything with 16 ga wire and EC-3 connectors which match up with the leads coming out of the 1222 or 9100 as well in my Eurosport. That way, everthing from the batts to the RX bus are good for 40 amps. My balance charge line on the batts is still typical 22ga with JR connector.
I still have to disconnect the batts if I am not going to fly for a few days as there is a small current draw even with everything switched off at the soft switch, but the 108 does break the + and - sides of the line so no problem charging both packs at once with my CellPro 10S. On my Hun takes about 5 minutes between flights, 10 minutes if I wait for a 100% balance.
The 108T has an intrinsic voltage drop of about 0.47-0.60v which leads to a bus voltage of 5.9-6.0 volts on the Data Logger with either A-123 or 5 cell NiCd or NiMh packs. I agree you can run A-123 direct which I do on my BARF and BCARF, but if you inadvertently stall a 3301 or 350 series mini servo with a fresh A-123 off the charger at 7.2, they will smoke faster than you can say W*F?

....been there.
Almost lost my BARF a month ago. Flying with a single 2 1/2 year old Li-Ion and brain farted. Left full flaps down after making some adjustments in trim and went to full throttle. The current draw from the flap servos led to a voltage drop which browned out my 1221 momentarily, power failed the P-70 ECU, and instant deadstick. Fortunately our field at the ends is very wide so saved it. No more old Li-ions for me......all 123.
http://www.youtube.com/watch?v=r13PX1r-H5w