I have setup a dual battery with a battery isolator. My question is can I put my trickle charger on the extra battery or will do you charge the primary battery and it transfers it over or does it matter at all?
put the trickle charger on your primary battery, your secondary battery should be charged by the stator when output is over 13.1 volts when the motor is running. Of course not all battery isolators are the same.
Long term storage? Y pig tail with clips. Jumper across both posts on the isolator and hook charger up on the other leg. Should work fine. Or just jumper posts and hook up to one battery. I like the Y better, because you are less likely to forget about removing the jumper.