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.
and Zoe the Wonder Dog(R.I.P.)
'07 Roo 23SS pushing an '07 Chevy Avalanche
Equalizer WDH and Prodigy BC