Bi-amp through receiver vs pre out to 2 channel for fronts

To be honest I don't follow how you're incorporating the sub or what that has to do with your surround speakers, but I'd still get fewer and better quality amp channels -- just make sure you replace the stock speaker jumpers with decent wire.  To me, better amp quality trumps biamping with a lower quality amp, but maybe that's just me. 

Are you getting the Atoll integrated or just a preamp?  I'm not sure why you're so high on biamping.  I think you're better off getting fewer but better amplifier channels for the same money and forgo biamping. 

Let me be blunt. Both the preamp and amp section of your (and almost all) AVR suck. They just flat out suck. If you replace one part, your stereo sound will be greatly compromised by the other. Period. People, especially when they’re relatively new to higher end Audio, tend to underestimate the importance of a preamp in the audio chain. Don’t make that fatal mistake. Get a good integrated and you replace both flawed components of your AVR at once. If you buy the Hegel H160 and compare it to your AVR I guarantee you won’t believe how much better your MA Gold speakers will sound in every conceivable way. There are no shortcuts here. Buy an integrated and get it over with in one shot. You’ll be thrilled you did.

It really depends.  You'll likely get the best overall bang for your buck by buying an integrated since you're only buying one box and need one less pair of interconnects (and power cord if you upgrade those too).  Then again, if you can space out the spending and potentially get a better separate amp and pre then you could end up better off that way in the long run, and it gives you a little more flexibility to tailor your sound -- for better or worse.  Choose your poison. 

If you’d really like the best sound possible in 2-channel, your best bet is to completely remove your AVR from the signal chain when listening in stereo. Neither the Pioneer’s amp section nor, just as importantly, its preamp section are doing you any favors in 2-channel sound quality. The easiest way to do this is to buy a dedicated integrated stereo amplifier. This way you can completely remove the AVR for more critical stereo listening literally with the push of one button if the integrated amp has a HT pass through feature, but you can continue to use your AVR for multichannel preocessing and to power your center and surround speakers. Believe it or not, you simply hook the AVR’s front L/R preamp outs to the HT pass through input on the integrated and hook the speaker outs from the integrated to your front L/R speakers, and you’re done. It’s literally that easy.

Not sure what you were prepared to spend on a new amp, but for around $1500 you could get a Hegel H160 or an Ayre AX7e available here now, both of which offer HT bypass and will significantly outperform your AVR for stereo listening. Bypassing your AVR completely in favor of either of these integrateds will likely far outweigh any benefits of just replacing the amp to bi-amp. You can probably buy some used shotgun biwire speaker cables down the road with this setup and get a good portion of biamping anyway. Just my $0.02, and best of luck.

Is 2-channel listening more important to you than multichannel or HT?