If you're asking purely about physically where to mount the second battery, I have a dual battery, single alternator system and I simply took the location in the plans on the firewall, made a tray large enough for 2 identical PC680's with aluminum angle hold downs and added aluminum angle bracing on the cockpit side of the firewall to compensate for the added weight, keeping in mind it has to be able to withstand the factory g limits. I have 2 independent master switches, one for each battery and independent grounds. When one master is off, that battery is completely isolated from the entire electrical system.
I have dual P-Mags, so operationally I'm different than your architecture. On cross countries, I fly on one alternator/battery like most non experimentals and keep the other off in case I have a failure of any kind. If I have a failure I can turn everything off and then switch to the other battery only and it will be at full capacity.