Where are the wires for the sub(s)? Are they in that bundle with the yellow terminated wires? What I'm guessing, and I'm only guessing because the pics aren't to clear, is possibly that 2 pairs of those wires are for rear speakers, and the other 4 pair are for an active front stage (tweeters and mids have their own crossover and power) BUT usually that's more of a high end install and the wiring you have there doesn't scream hi end. I may have missed it but what do you have for speakers in the doors?
I'm also confused on what the relays would be for back there.
Do you have any pics of the whole panel to give an idea on how it was all laid out? The fact that there's 3 pair in one bundle and 3 pair in another, that are that far apart is also confusing.