Strangely enough my son has the same problem, he has a P100 pick up and I wired a relay to the ignition circuit, the only problem is he tends to have the radio on when its parked which of course means the batteries are connected together.
I was going to try connecting a relay to the alternator exiter terminal so its only switched in when its actually charging, have'nt got round to it yet though.
I replaced the engine in it last year and the working battery isn't connected to the charging circuit at the moment, but he has a good 100 ah deep cycle battery on it which only needs recharging about once a week.
Peter