I, too, have a blended system, but my AVR is an older Denon AVR-X4000 (which was their flagship AVR at the time). The important thing is that your Yamaha appears to have pre-outs. I run my Denon pre-outs through a Parasound P5 preamp then to a B&K EX-442 Sonata amplifier to power my Maggie MMG mains. My surround speakers (Elac Debut 2.0 B6.2) come off the P5 and run through an Adcom GFA 6000 5-channel amp (nothing else is connected to it but those two surround speakers). I don't use the internal Denon amps for ANYTHING - I don't run a center channel speaker. Denons run famously hot already, and mine still does, even with all the power handling offloaded to two separate amps. If you don't need surround speakers, great. You probably don't even need a separate preamp, but I wanted one strictly for two channel music (or 2.2, as it currently stands). I'd say that, from my angle, one of the easiest ways to improve your sound is to get your mains off the Yamaha AVR receiver and feed them from a separate amplifier. That would be my first move. If you don't want to add another component (which certainly makes sense ) then the alternative is to do as suggested: get an integrated with a HT bypass. The key to these blended systems (and getting them to sound their best for their respective applications) is to have a preamp somewhere in the chain with a HT bypass. Gotta have it, IMO, to carve out as much of the "video" signal path from the music signal path.
Luck.