Turn the packs so the plugs are on top. Velcro them together so that the bottom pack's plugs are just clear of the top pack. Put the plugs of both packs at the same end of the tray. Use a foam spacer on the opposite end so that the battery doesn't shift forward.
Like this:
==============P
X==============P
That's how I've planned to run mine from day one. If that doesn't work out I'll be buying new packs too.
Chris