That Yamaha really is a great price, and any end of line stock is a great idea. I got my current amp from Superfi, it was the last one the chain had and as a result was £700 down from £1400! The replacement model was out and at £1400 but sonically there was practically nothing in it.
Don't worry too much about placement (though it is important) either as all the good modern amps have their own auto calibration to tweak outputs. If one speaker is a touch out of place to the others it will be compensated for.
Personally I would say that a good front stage with a solid sub is the foundation with rears being secondary to that.