Because the battery is the source of the electrical potential, you want a fuse as close as possible to it.
If you have a battery under the hood, in the trunk or under hood and in the trunk, well the fuse(s) should be close to that(those) battery(ies).
Because the electrical device is another item you want to protect you put a fuse as close as possible to it also.
Most aftermarket components have fusing so you don't have to add an additional fuse close to the device you want to protect.
The fuse close to the battery protects the vehicle as well as other components.
Should wire from your battery become over loaded you can burn up the vehicle with only a trunk mounted fuse.
Anthony B. Davis
2Deep2 Silver SVT
2002 IASCA SQ Ult Ama 601+ World Champion runner up
2002 SLAP dBQ Champion
2000 USAC SQ World Champion
2002 USACi SQ World Champion