Welcome to the forum!
I'll start with your second question. If it were me, I'd connect two of the Bose 201 speakers to the Front left/right speaker terminals on the Pioneer, connect the remaining two Bose 201 speakers to the Surround left/right speaker terminals on the Pioneer, and then configure the Pioneer for the four speakers. Configuring the system is easy - just follow the instructions in the manual to run the automated MCACC set up routine. It should set the center channel (which you don't have) to "phantom" (meaning, it will use the two front speakers to mimic one) and set all of your speakers to "large" so that they'll play the full frequency range (because you don't have a sub hooked up, at least, you don't mention one for this set up).
As for using your Yamaha in a second zone, the way to go about it will depend on some things. First, if you are going to use your Bose speakers, then the Pioneer will be set up so that it won't output any audio through the HDMI output (it can either play the audio itself or output it - it can't do both). If you want to use the HDMI output from the Pioneer for audio, you'll have to change that in the menu settings every time. Do your blu-ray player and cable box have analog audio outputs or digital audio outputs? If so, it might be best to run HDMI to your Pioneer, and run the analog (or digital) audio to your Yamaha. We can talk you through that if you're interested.
