Without wanting to sound patronising, Everything worked ok until you fitted the woofer, then it didn't. That suggests that there is either something wrong with the woofer itself or the way you fitted it.
The best thing you can do now is completely disconnect the subwoofer and the stereo and make sure all the fuses are fitted and intact
Now switch on and check everything works
Assuming it will,
Check the wires in both the multi pin plugs that plug into the stereo.
Any signs of wear or shorting.
Don't be fooled into thinking that just because the stereo works, the wiring is OK, the one i took out had 1 earth and 3 power feeds, 1 main (red) and 2 auxilliary. God knows why (maybe one for the subwoofer???)
Stereo was working fine but one of the other feeds was shorting out and blowing fuse 12.
Insulated it, Jobs a good un !
You really don't want to be driving without fuse 1 (warning lamps and gauges, Coolant Temp control unit!!)