#1 you got a heck of a deal on one of the best chargers made
#2 you can do it one of 2 ways. You can hook each side to each battery seperatly and leave your jumper in place.
#3 you can hook one leg to one trolling battery and leave jumper in place and still charge both batteries and hook the other leg to cranking battery. Depending on amp out put will determine how long it takes 1 leg to charge both batteries.
#3 is how I have my 2 bank 5 amp per bank set up on my 12 volt system with 2 batteries for trolling. Never had a problem charging both overnight except 1 time in 5 years.
Proud Member of Team Geezer
Charlie Weaver USN/ENC 1965-1979