My previous setup used the H6 board with a HT sub and studio monitors. You connect your mains to the L/R channels on the STX II. You connect your subwoofer to the center channel on the H6. Center channel is the real channel for subwoofer. You can use the sub channel but you will have to swap center/sub channel in software so might as well plug the sub in the center channel.
There is a way to make 2.1 run perfectly even though the Xonar and windows thinks you are in 5.1 mode. For me, I uninstalled Asus' drivers and got the Xonar unified drivers. During the installation something will come up with stereo upmix or something like that, make sure it is turned off. After that all your video games, movies, music should run 2.1 flawlessly.
With stock Asus drivers, many video games would think I am in 5.1 mode so I could not hear any dialogue and the sound overall was screwed up because I only had 2.1. With those drivers, all my games worked in 2.1 just fine.
You also need to use the built in crossover through the software, otherwise you will get no bass from the sub.