Your Yamaha is a 7.1 receiver... meaning it can amplify 7 speakers. 5 speakers, (for a 5.0 or 5.1 system), are hard wired. Meaning they are not configurable. They are permanently assigned to Left, Center, Right, Left Surround and Right Surround.
Your last 2 channels are configurable. It means you can assign them for different uses. Its connection on back of your unit looks like this:
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You can see it's even called "Extra Speakers", and your choices are Zone 2, or Front Presence, or Bi-amp.
Your AVR also has a dedicated Zone 2 output, but it's a pre out... meaning it is not amplified. You cannot run it directly to speakers. You need to run it to an amp, then from the amp to the speakers. Your Zone 2 pre out looks like this:
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And there are additional pre outs right next to this so you can have a whole surround Zone 2 if you want.
So you can run a 5.1 system with the Front Left/Right speakers bi-amp'd, but then you'll have to use your pre outs, (along with another amp), for your Zone 2. Whichever you chose, you'll have to go into Settings on your Yamaha and tell it how you want it to assign the "Extra Speakers".