I hate those darn crimp on butts, solder and heatshrink are definitely your friend to clean that up..
On your signal wires (RCA), you have it plugged into the right plug, but on your other cable, how many pins does it have total? The one that goes to the stereo should have like 8 pins total (single row of pins on the connector), that's justto power the radio, illumination, etc. If you're using the cable that has a total of 14 pins (6 on top, 8 on the bottom), that's JUST for the audio out, and amp signals TO the amp. That stays plugged into the amps left most plug only. The thinner plug goes to the radio to supply DC power/ground/etc to the stereo, and the small 8 pin connector goes to the RCA adapter. It's POSSIBLE you have another 8 pin plug in there that would have gone to the external CD player if the car was equipped with one, not 100% sure if it's the same as the RCA adapter plug or not though(been a while since I pulled all that out of my car, so can't remember if it was the same, or slightly differrent).
As far as the amp connections go though, that larger 14 pin plug goes into the dash center amp, there's a smaller plug in the middle of that amp that runs the rear sub amps, and the right most I believe is where the RCA-adapted connection goes (uses the factory wiring in the harness to connect there, since it's female on both sides).
IF you're getting sound when you connect the wiring for the speaker level outputs into the same connector you're using for power on the radio now, you're using the wrong connector I believe...
I ended up just ditching the mach460 amps, and used the tweeter output cabling to a small clarion 4 channel amp in the dash, then installed good sets of seperates in the front doors and rear boxes on my 2000 convertible. Just use the wiring from the tweeters to the seperates crossovers, then the crossovers wiring to each speaker and done. Sounds WAY better than it used to, and much easier to manage. I just need to run power wiring and RCA's to the trunk for my sub, and I'm going ground everything directly to the battery (I have a bad ground somewhere, I'll get it sorted out eventually, but grounded to battery works fine without any alternator whine). That's on my list of crap to get done this weekend, lol.
I also have a full set of Mach460 amps (2 rear mono amps, and the front 4 channel with internal crossover) that work fine if you need them. Also make damn sure you either use resistors or some other means to adapt the power on signal from your stereo to the mach460 amps, as they expect 6v, and modern radios put out 12v. You'll get a nasty pop every time you turn on the radio if you don't...