There are battery trays available for the diesel models that fit between the coolant bottle and the motor. I am running a ctek d250s mounted on the fire wall above the abs setup, tight but it fits. I went this way because I also run solar on the roof and the ctek handled both the solar and the dual battery management, can be had for about $250 on eBay. As far as batteries go at the moment I run a plain old deep cycle, it does the job well for the time being but when it dies I'll be fitting the biggest AGM I can fit.
Shane