Yea, if it's aftermarket you'll want to hook it up to the red wire going to the deck, or the designated "remote" wire, which is usually blue. Some decks turn the sub amp off via an option built in, which is when you'd want to use the designated remote wire for sure.
If you're using a stock deck I usually tap into the harness behind it.. take a tester (one bought for this task, or an LED/resistor or something that runs on 12v), ground out on side of it, poke the lead into the hole on the harness of wires that look probable (usually either thicker ones, or red/yellow, or both). Turn the key to accessory and if your tester lights up, use that wire, if it doesn't, keep testing wires. Make sure the tester goes off when the key is turned off, otherwise your amp will be on all the time.
Never done the fuse thing before.. but if you do just make sure the fuse loses power when the key is off.
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