It depends where the batts are in relation to each other. Grounds should be kept as short as possible. You can ground them together or separately, what you need to consider is A) wire length, clean ground connections, C) ground potential.
The wire length is pretty self explanatory. When you do connect the ground to metal, make sure it is bare metal and use some sort of protection over the connection to prevent rust/corrosion. As for ground potential just make sure you are using a piece of sheet metal or frame that is of low resistance; I.E. not a body panel that is welded to the unibody like fender wells. If you have a DMM, hook a lead to the negative terminal of the main battery and use the other to check where you want to ground. Just look for the lowest resistance and try to have the same ground potential for both batteries.
If the batts are close, ground them together, just use appropriate gauge wire.