For the purposes of testing an amp it really doesn't matter where the fuse is. In fact it doesn't matter whether you have a fuse at all..as long as you've got a fire extinguisher handy in case the amp is shorted out internally.
For the purposes of installation, the wire to the amp should be fused with an inline fuse as close as possible the source of power that is connected to. Usually that's the battery.
A fuse only protects things downstream from it, and if that wire feeding the amp were to get pinched and shorted somewhere, you want the fuse to blow instead of the wire heating up and catching something on fire.
