There has been much debate about this a few months ago...
But no, it does not matter if you leave the connections on the batteries to charge them, and I also stand by my opinion (a few will disagree) that it does NOT matter which battery you hook the charger/jumper leads to, assuming you have heavy enough cables (factory size or larger). If you have the proper size cables running from one battery to the next, then on to the starter, the whole arguement of having to hook to the passenger's side battery is essentially a moot point. Copper cable is obviously a very good conductor with minimal line losses, therefore it is an insignificant difference as to which battery you hook to. Just use whichever is more handy for you.
1994 Ford F250 4x4: 7.3L IDI factory turbo, supercab longbed, E4OD *DEAD*. ZF5 swap,Dana 60 swap, GM 14 bolt rear w/ 4.10s, 4" exhaust from stock downpipe back to a 5" stack, IP maxed=1100 degrees max pulling uphill, "modified" wastegate=11psi max,99+ F450SD cab/chassis leaf springs in rear
2000 VW Jetta TDI = 48+mpg
Member of Indiana Air National Guard 122FW MXS