The colors don't really matter and there isn't any polarity issue per se regarding speakers and amps, what counts is making sure the speakers are in phase. If your speakers are out of phase, then the wave crest of one speaker coincides with the trough of the other and the sound tends to cancel out - the same principle is used in those Bose sound-cancellation headphones they advertise on TV.
That having been said, the easiest way to make sure everything is in phase is to run positive to positive and negative to negative for each channel. However, if you ran positive on the amp to negative on the speaker and vice versa for BOTH channels, you would still be in phase and everything would be OK soundwise, just a little confusing schematic-wise.
The short answer is to check the connections on the speakers (color and polarity), write it all down, and duplicate the connections on the amp.