Yes, I think the bypass - to include capping off the stock B+ line - is a good thing. I also believe that bypassing the ignition wire to the starter solenoid via a 30 amp relay is superior. I did both with my Sporty and documented the mods in my dual batteries with isolator thread. Check out the photos at the bottom. They may help you plan the B+ bypass...
-------------------- 1997 Sportage 4x4, auto-trans, Warn manual hubs, 4" UPYOURKIA front lift, TJ 106AA rear springs, 2-5/8" body lift, 31x10.50 treads, SmittyBilt SRC front and XRC rear bumper, swing-out tire mount, OBX LSD front diff, Track Finder rear locker, 5.38 R&Ps and... really crappy gas mileage!
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