The wiring goes from the HU up to the tweeter, and from there down to the door speaker. The second plug is simply the one that goes down there - if you look at where the two plugs where plugged in (look at the metal connectors and surrounding wire traces), you'd see that it just passes the signal straight through from one plug to another.
The crossovers simply separate out the low notes and high notes, so you can send the lows to the woofer, and the highs to the tweeter. This should greatly improve the sound quality.
You shouldn't plug the tweeter in directly like it sounds like you have! The HU will be feeding it Bass notes as well as the treble ones it's designed for. the OE tweeter had a filter built-in, but you must use the crossover boxes you got with the new components. There is a risk of damaging your tweeters if you turn the volume up before installing your crossovers with it like it's currently wired
Basically, the wires which are coming from the head unit (the ones you've wired into the tweeter) should go into the input of the crossover, then seperate wires should go from the crossover Tweeter outputs to the tweeter, and from the woofer outputs on the
tweeter crossover to the woofers.
The way I wired mine was to take off the lower bits of the dash (the bit under the wheel on the drivers' side, and the entire glovebox section on the passenger's), and feed the wires that go up to the tweeters down into the dash so they were sticking out the front. I then wired the wires coming from the HU to the INs on the crossovers, and the wires that went to the door speakers into the woofer outs on the crossovers. I then needed some new wire for the tweeters, but mine came with enough wire to thread down through the dash already attached (which I connected to the crossover's tweeter outs obviously). This let me install the crossover boxes behind the dash trim that I'd removed (just attached with some decent tape, but they're positioned in such a way that screwing the dash trim back on effectively holds them in position, so the tape was only required to hold them loosely in place).
I hope that's fairly clear. If not I'll try to go whip my dash off and take some photos for ya, so you can see what I mean
It's no big deal - only about 8 screws in total I think.
(Whoops.. Just re-read that, and I suggested wiring goes from the tweeters to the woofers, but it's from the crossovers to the woofers... Strikethru'd the typo..)
