Attaching a fuse to a new set of batteries?

Typically all the fuses go at the positive end of the battery (or batteries). There's no real need to fuse both ends, at least in any ordinary application, as interrupting the current at one pole will interrupt it at the other one as well (thanks to Kirchoff's laws and corollaries). For main fuses, it's perhaps not quite so important which end is fused; but for branch circuits, with lower and varying capacities, shorts to ground (as in the framework in general) are one of the big things that is being protected against, and fusing the ground lead of the branch circuit does nothing to protect against them while fusing the positive lead does. For consistency, if no other reason, fuse the positives.

Of course, adding additional fuses is harmless (from a safety standpoint), but it does add more cost and connections that may work loose and things to check when stuff stops working.