sub amplifier, loc or speaker level in?

I agree with the above but if you are happy with the existing deck and changer, you may not be changing over to an aftermarket deck while you own the car.  I would put some faith in the Alpine's built-in LOC in this case, because Alpine is a quality manufacturer.  Run test wires to see if it all works together first.  The speaker wires don't have to be permanently installed for a test run.  If it does work, that is, if the Alpine's LOC accepts the deck's voltage and everything works, then go with the built-in LOC.  This is the lowest cost solution and the Alpine's LOC may be as good as or better than most common fixed-voltage LOC's you would pick up at the store.

You will probably want to run the speaker wires to the front speaker locations (or wires) instead of the rears so that the deck fading control doesn't diminish the sub output along with the rears.  But running long lengths of regular speaker wire through the car that connect to the amp input is an invitation for noise pickup, so instead of using regular speaker wire use the twisted pair variety.  You can buy it or make it yourself.  Pos and neg wires are twisted snugly around each other for the entire run.  The wire will still pick up noise but the twisting will effectively cancel it out.

trocker, your car or not...when you install wiring for a system you run the wires hidden.  Same goes if you are tapping the rear speakers: hide the wiring.

If you don't adjust overall soundstage balance by using the fader then it doesn't matter whether you use the front pair or the rear pair.