i don't think that's a stock cover, though it might have been an option at one time. that Roo is a 2006 or older.
most Roo's have just the tanks covered, not the battery.
on my Roo's A-frame, the battery was mounted across. i mounted the two new ones, length-wise and they fit with the boxes bolted and a strap around both boxes.
to get two batteries, you'll have to ditch that cover of yours.
__________________
Dan-Retired California Firefighter/EMT
Shawn-Musician/Entrepreneur/Wine Expert
and Zoe the Wonder Dog(R.I.P.)
2016 PrimeTime TracerAIR 255, pushing a 2014 Ford F150 SCREW XTR 4x4 3.5 Ecoboost w/Max Tow Package
4pt Equal-i-zer WDH and 1828lbs of payload capacity