You could either:
(A) Use the PC to do the bass management and control the volume. This would involve setting the volume on the sub and volume on that amp so that the sub and speakers were matched well, then leaving them where they are at and controlling the master volume of your music using the PC's volume control. You would set the PC up for two speakers and a sub, run the subwoofer connection like you've done, and run the left/right line-level connections from the PC to the line-level inputs on that amp.
(B) Set the PC up so that you have two speakers and no sub, run the left/right line-level outputs from the PC to that amp, run the left/right speaker-level outputs from that amp to the speaker-level inputs on your sub, and run the speaker-level outputs on the sub to your speakers. You would then use the controls on the sub to set the cut-off frequency (for which low frequencies are handled by the sub and which are handled by the speakers - something like 80-90Hz is normally a good start), and you could use the volume control on the amp to control the overall volume of the music. You can do this because that subwoofer will accept speaker-level inputs, filter out the desired frequencies, and send the filtered signal on through to the speakers.
