Don't get number of channels mixed up with the number of speaker outputs!
Your MX-1000's are 2-channel (stereo) amplifiers. They have two identical amplification stages, one for the left and one for the right speakers. A 6-channel amplifier would have 6 amplification stages, 6 sets of inputs, and 6 sets of outputs.
What your MX-1000's have are additional output terminals and selector switches. That way you can wire up multiple pairs of speakers and select between playing each pair separately or combined. However, your amplifier power and current handling capabilities stay constant. So, you have to be careful when running multiple sets of speakers off of one amp. Running multiple sets of speakers will affect the total impedance load presented to the amp, and with too low of a load you risk burning out the amp. Using one amp (or multiples - e.g. biamping) per speaker pair will ensure that each speaker can receive maximum power with the easiest load on the amps. I would highly suggest reading through the whole manual for a better understanding:
http://www2.yamaha.co.jp/manual/pdf/av/english/SepA/MX-1000U.pdf
Anyway, GREAT score! I am looking forward to seeing the refurbishment process. When you get everything going take a look at horizontal and vertical biamping and how you could apply it to your system. If you are interested in surround sound it might even be really cool to do a 4.1 setup with a "phantom" center channel. You have a lot of great possibilities with that system. :yes: