Quick question, Can I use a receiver AND an external DAC for a 2.1 setup?

I have a 2.1 setup, just the standard left/right bookshelf speakers and a subwoofer. I am using a receiver to output the signal to my subwoofer via LFE out, and also the speakers. The source is my computer. 

It sounds fine but I find that "Direct" mode on my receiver outputs more live and natural sound than the "Stereo" mode. Stereo mode allows for me to utilize my subwoofer, change the  bass, treble, etc. since all the processing is done on the receiver/amp. Direct mode seems to sound better (at least more natural and less saturated) even without an external DAC and just coming directly from my computer's onboard "headphone out". Is there a way to get my subwoofer working in this mix? 

In the case of people getting external DACs to convert the signal from their computer, how would I get that to divide between my speakers and subwoofer if I have to leave it in "Direct (or Pure)" mode on the receiver? If I don't use Direct mode, I understand that all the work done by the external DAC is rendered useless since the signal is processed again by the receiver at the last stop. 

Well I'm thinking about adding a DAC, I don't have one yet but I am guessing it would be digital optical out from my PC to the DAC. And DAC analog out to the receiver. 

It looks like there's no way for me to run Direct mode on my receiver with the subwoofer. It only goes to the front left/right speakers. I guess I can bypass this by using a speaker level setup with the sub instead of the sub LFE out so I might try that. Only problem is I can't use the remote to control the subwoofer channel volume if it gets too loud. It'll just be integrated into the setup. But my sub has a volume knob so small price to pay to listen in direct mode. I'll update to see how it sounds.