I'm not familiar with that Yamaha so I'm giving you generic instructions. Set the sub crossover to 80hz. I like to route all of my bass to the sub instead of just the LFE channel so I set my speakers to "small" even though they are tuned to 35hz.
Now you need to calibrate without any automatic tools. Set your distance with a tape measure. I sat my wife down in my spot and measured the distance from her head to each speaker. I then entered it into the receiver. What does that do? It assures you that the sounds get to your ears at the exact same time despite the different distances between speakers. Set your levels with an SPL meter. Don't have one? Download an app for your phone. It doesn't have to be set to 85db, they just need to be set all the same. For my cousin, I spent 5 minutes with his receiver and the internal test tones and it was done.
If you want to get even more detailed, let me know. I run a digital parametric equalizer on my sub so that my in-room response is + or - 3db from 100hz to 17hz with significant output down to 12hz. That sounds like a lot but the EQ is less than $100 and it made a HUGE difference in my bass.