for sure you are not suppose to cut the carpet...... may need a micro trim but no cutting
stock truck with a bench seat will have the harness running on the right side of truck then passing under the front passenger seat and then to the console....... left to you 2 options: you extend the harness and running it as the original should be or.....under the carpet straight from the middle of dash to the bench seat
second option will be easier but with time ( and sometimes it's ****ing fast ) will cause problem because anything can fall on the harness as it is not hide from foot , boot, bag, etc etc,
doing harness as original will take you more time ( to do a really clean job ) but for sure the best thing to do
harness should not interfere with any parts, it's also should not be a problem if you have to change something close to the harness,
for the sub ,,,pretty sure you can install it under the bench seat ........some place there ,or under the rear seat on right but you will see it when the rear seat will be raise....
again sorry for my poor english . lol i even not understand myself but hope it help