Lewinski,
I've used several different configurations, but I'm currently taking the digital signal out of my QSonix server straight into the Onkyo via coax. The Onkyo does all DSP including x-over. The twin sub out of the Onkyo goes straight to my Rythmik subs and the main out goes to (at the moment) a pair of Cary 805s and on into a pair of OHM 100s. Sometimes, there's a different amp/main speaker combo, particularly if I'm using my Maggie MMGs, which require more grunt than the Carys can deliver.
BTW, I've previously used both of my current stand-alone DACs (Cambridge DAC Magic and Benchmark) for conversion, but - as I've noted - simplicity is important to me and I prefer the simplicity of one box. As to SQ, it's audibly different with each DAC (especially Benchmark vs Cambridge) and a matter of personal taste, but I like the sound of all three options and settled on the internal Onkyo DAC for the reasons stated above.
Further, BTW - there's an upgraded version of the Onkyo from one of the specialists (Upgrade Company?) that offers an in-home trial. At the moment, I'm kicking the idea of a trial around just to check out any potential improvements. If I pull the trigger, I'll post my impressions