you are doing exactly what I did with my butler robot chives - erobots.blogspot.com
Look on the right hand side of the blog , there should be something about relay controls
You need a total of 8 relays for this to work - four per motor .
post up your schematic and I'll help you out
what kind of R/C unit are you using , because you will probably need a MOSFET to drive the relays for certain R/C stuff
I have two 24V motors running at 12V just fine . Which motors are you using ?
The two 12V batteries need to be wired in parallel to give off 12V. How much current do your motors draw
and finally what project are you building , so we can help you out better.
Ask anything you want on this subject , because I am almost an expert on it ( I've done it before many times)