One thing you can try right now is running the Squeezebox directly into the power amp, using the Duet's level control, and see if there is an improvement. Don't worry about bass management right now, you are looking for higher resolution in the mid to upper frequencies.
If that's an improvement, then look at a HT bypass setup, using a passive pre for the two channel music. An add on DAC after the Duet should improve things, maybe one (tubed or no) with a level control? For more $$$, a decent active preamp with HT bypass will work also.
I wouldn't recommend running the Squeezebox into the power amp as a permanent setup, although I did it once using a SB 3 (Classic) into an Aragon amp to MMG speakers. Heard horror stories from folks of the programming going haywire, suddenly sending a full voltage signal out of the Squeezebox. Plus, if you keep the signal already at full gain, controlling the level downstream, you know you are getting the most bits performance.