Bedway,
You definitely want to put the fuse on the hot side so pulling it will kill the whole circuit. The preferred place would be between the battery & the switch.
Electricity will go where ever it can, so if you kill the whole circuit you won't get any surprises when you think the circuit is disabled. If you fused the ground side, a short to ground would allow the motor to still operate when you think it is disabled. Be very careful.
Theo
ex-submarine electrician (BIG batteries)