The best way is to get a new headunit and dump your old one. Your stock headunit will never match the performance of even most poor aftermarket headunits.
However, if you want to keep your old headunit, the best way to connect an amp for a sub is to use an LOC converter which draws the sound from both rear speakers. Some amps like my Dual have an internal LOC converter so all you need to do is run the speaker wires to the amp and don't need any RCA cables.
The remote wire can be done like has been said above.
Hatch Nation #13 : Rally Revolution #13 : ROTM Jan '13
It's Bryan, not Brian
RSVT-170 Build in Progress
Derusting Rusty Build in Progress