Jason Ponder

Hello all. I'm trying to put a better stereo in my 02 miata, and thought that i had bypassed the amp successfully, and then I found that all the wires to the bose tweeters and woofers are the same yellow/green(+) and green(-). I messed up one woofer along the way, so I took the woofer from the right door, and hooked it up in the left speaker slot, and am running it with a pioneer. but that speaker only responds to right speaker controls (balance, speaker level). At the same time, both tweeters work, and both are wired with the same speaker wire colors.
I tried hooking up an aftermarket speaker into the right door tonight, but got no sound from it. I'm at a loss at this juncture. Any help would be appreciated