Having placed tow GC-1 AGM batteries under my hood in a new battery tray I fabricated myself, I can say that I did fabricate the battery tray to sit lower than the stock auxiliary battery tray by 2-3”—necessary to allow adequate clearance for the batteries. I also bent the harness for the ECM to an upward and forward position (stock position is beneath the battery tray), mounting it on the front side of the new battery tray; this was to create the space to lower the battery tray position. 6v GC-1 batteries are taller than the stock Group 49 batteries, so even one 6v battery won’t fit in an unmodified stock battery tray.
I would suspect that if you already have two 6v batteries mounted under the hood, you already have an aftermarket battery tray, so you should be down to a point of just taking measurements for what you already have, and then compare that to the published dimensions of what you’re contemplating. (Do remember to leave adequate clearance between the tops of the batteries and the hood so as to avoid unwanted sparks and fireworks!)
Also, for consideration, look at the battery weight. These GC-1 batteries weigh about 65 lbs each, and "manhandling" them is a burly person's job. I used a cherry-picker shop crane to gently mount my two batteries in the tray.
Rock Doc