Your main speakers, the DOGG Digital Audio ones, are a 'white van special' brand. No offense, but they are junk designed to defraud people: see
the list in this article. The speaker positioning is also not great. You generally don't want speakers tucked away in corners. The reason is that the sound reflects off of sidewalls very strongly and causes a lot of diffraction and other adverse acoustic effects.
The subwoofer situation is problematic. You are mixing different subs with very different performance characteristics, and that can cause more problems than any good. The JBL powering another sub as a passive radiator is disastrous. It may be making sound, but I guarantee you it is anything but accurate bass reproduction.
If I were you, I would first replace the front left/right tower speakers with something more legitimate, maybe some inexpensive but decent bookshelf speakers. I would remove the Logitech sub and non-functioning passive radiator sub. I would position the front left and right speakers in a more optimal way; I would bring them forward away from the walls while trying to keep them from being close to nearby surfaces.
Here is a good example of speaker placement for a desktop PC in a small room. Try to place the speaker's height where the tweeter is level with your ear height in your normal seating position. Try to aim the speaker to face your listening position.
Anyway, I don't mean to sound too critical, and I appreciate your enthusiasm in getting a better sound system. It's not easy on a tight budget but it is possible. I think you can get a significantly better sound with just a few changes.
The PC case is pretty kick ass, by the way, and the whole setup looks like a pretty fun battle-station overall.