I have gotten my desired result. I don't know why I didn't try this before, or, if I did, why I didn't think it was the solution.
I set the software to Stereo Direct under the Speakers/Headphones section.
Everything sounds beautiful and I have the expected output I was looking for.
So I have been struggling with a new 2.1 setup for a couple of weeks now and have no idea what else to try.
The setup is as follows:
Amp: SMSL SA-60
Sub: BIC F12, Volume at 5, Crossover at 100hz, set to Dolby Input [not 5.1,7.1, etc].
Speakers: Infinity Primus P163
Soundcard: Creative SB Zx...