The Xonar ST will be an improvement over the onboard audio for using headphones. You can then plug a receiver up to the line outs, and still use the headphone out by switching between outputs in the software control panel for the card. To get the best out of that soundcard, use the Xonar Unified drivers.
I've never heard of that comparison before regarding Marantz, HK, and Onkyo. Perhaps you are looking at reviews of HK AVRs, not their 2 channel stereo receivers? Here's a pro review of the HK 3490. No comments about movie sound there. The HK 3390 would be the same in terms of SQ, just a less power and without the built in DAC. If you look at all the reviews of the 3390 and 3490 on Amazon, I doubt you'll find people saying that they are best for movies.
Since you have HDMI out and optical out, you could elect to go with an AVR. Advantages include bass management, ability to add more speakers to build a surround system, and room correction software. If you do, I'd look at Denon and Marantz models that have Audyssey MultiEQ or better versions.
Try MusicBee for a music manager. It's free to download and use. Easy to configure. Has a following here on head-fi.
Be aware that if you go with the Polk sub, might not work very well to use the wireless. Wireless causes a very, very slight delay in sound. Lot of people using the wireless subs are doing so with AVRs which can adjust for that difference. A 2 channel stereo receiver or integrated amp will not be able to.