Run a thick gauge wire (4 gauge should do it) to your amplifier. Put a fuse 18 inches or closer to the battery, then continue the wire to the amp. Run RCA cables from your CD player/head unit to the amp. Run the antenna wire (usually blue colored) from the CD player/head unit to the amp (it turns the amp on). Run the speaker wire from your speakers to the amp.
Mount it in a dry location (make sure your trunk doesn't leak, if you aren't sure, put it under a seat or something).
You can probably find a hole in the firewall in front of the engine, you can run the amp power wire through there. If not, drill. But be careful.
The trunk firewall is usually thinner than the engine firewall, but it usually doesn't have a hole to work with. Just pick a place inconspicous.
Make sure everything is hooked up right. Wrap any frays with electrical tape. Wrap any ends that don't go anywhere with tape. Don't leave hot wire laying around.
Good luck!
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Off the record, on the q.t., and very hush-hush.
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