Search out the bulk charging threads. Methods sells some good equipment for it, in for sale new.
I can't or won't try to explain it, since I like the idea that I get to inspect my packs every charge. Wow, that ones hot after the ride! Lets see why. To me it beats, why is the garage on fire?
You can deal with it though, by having each pair of packs plugs on the outside of the case. That would allow charging of each pair at 6s. Use a paralell series harness type setup to make the switch. An internal sensor could give you packs temp, so you can tell when it's going horribly bad in there.