Whoa, so many answers. Obviously you can tell I did not put the system in the car. I traded a '03 Mustang for this '68 Mustang. It came with the audio unit already in it. I know generally how audio works, but once you get into amps I get sorta lost. My '03 had dual stock amps, but I left them alone.
I am going to try those recommendations later, I cant get into it right now. And I can post some pics of the connections on the amp, but I really dont know where they go. Mainly because I cant get into the custom box, without taking it apart. Or at least take the sub out.
Here is a pic of the sub, with the back seat out;
As far as the wires go, there is only one set of RCA cables plugged into the receiver. But on the amp... there are two. Not sure why. Then on the other side there is a whole slew of cables connected. Again, Ill get some pics probably tomorrow. I do not use any of the speaker wire, its all zip tied up. I only use the yellow for always on. The red is to the ignition to turn off the power. The black is ground. And the blue/white is to the amp. Again, it is hooked up exactly as the last radio, which was a Pioneer too.
I tried messing with the settings, I will unplug it altogether an reset it. There is a Sub 1 and Sub 2 setting. And you can set it to normal, reverse, or off. Off makes it to where there is zero sound, because only the sub is putting out sound.
I really should take the whole thing apart and see whats what. But from looking at it, it looks like its put together really well. The custom box is made nice and tight. There is a sealer in the hole for the wires running to the amp thats in a box, looks like hot glue. The wires and cables look to be all new, and are all hidden. But until I go, I wont really know what I have. But I really dont care as long as it just works. If I cant get this to work, guess Ill move up to a higher end Pioneer. That Sony worked just fine, but like others said it just didnt sound as good. Which really surprised me. Mainly it was the bass. I did not change any setting on the amp, before I tried to radio. I literally took the Sony model out, unhooked the four wires. Then hooked the same four wires up to the new Pioneer, and ran into this problem. At that time I messed with the sub settings. One at a time, putting it back to where it was before I changed it. Didnt do anything, but then again I really didnt know what I was doing.
Thanks for all the suggestions, sorry Im such a dunce with this. I am going to try either tomorrow or Thursday.
edit, remembered I have this. This is used on the front right speaker that you can see in an above picture. There was one on the left side. The guy took it out for some reason, and I left it out because I want to put manual in it, and it would be cramped. Not sure how this box is used, but all the connections have a wire in them, then somehow it makes it back to the amp. Crappy cell phone pics.