bass lover has it basically right. Fuse the wire as close to the source of power (battery) as possible, to protect the wire from shorting out, melting it's insulation, and burning your car down.
Fusing for the amp is done as close as possible to the amplifier itself (usually internally). If the amp is rated @ 200a, and your wire is also rated @ 200a, then 1 200a fuse inline on your power wire, as close to the battery as possible, will do the job for both the wire AND your amp. In THAT case, it'd serve the same purpose - and if you want to, you could fuse your wire much lower than it's rated for, which would result in the same situation.
For example:
1/0Gauge wire, amp max 100amps.
Obviously, 1/0 ga can handle well over 100a. So you'd fuse the 1/0 for it's maximum - then your amp would need a 100a fuse too, to protect it.
You COULD just put a 100a fuse on the 1/0GA wire, then the same fuse protects the wire AND the amp....as long as that 1/0ga wire isn't used for other amps, that works fine...but if you split that 1/0 to 2 amps, and each needs 100amp max for themselves... now you need to fuse separately the wire itself at it's maximum rating - then fuse each again after they split to the amps at the amplifiers' 100a ratings. You can see how people can get confused about whether or not they serve the same purpose...they can, in some cases. Most of the time you have 2 amps run on 1 large wire run - and THAT's where people get the idea that they are different - because in that case, they are; the large wire needs it's own fusing, and then the 2 amps need their own. If you only ran your wire for a single amp, then the same fuse can protect the wire and the amp.