Being omnidirectional really has very little to do with it. A sub is non-localizable below 80Hz for the most part. However, if you put it right next to you and the speakers are 20 feet in front OR you set the xover to 100-120Hz, you WILL tell where the sub is. Even with an 80Hz xover point, assuming a 12db/octave slope on the xover, you'll have a lot of bleedover that is localizable. For example, let's say that your sub is playing at 90db. Now, with an 80Hz/ 12db/octave xover, 160Hz will still be at 78db.
Realistically, if connected via an LFE output, there shouldn't be much of anything above 80Hz. If you're using a common xover/bass output that's a different story. In either case, there are harmonics that the sub produces that are well above the 80Hz range that are localizable and nothing you do to the xover will do anything to change it - they're caused by the cone resonances, box resonances, etc.
Also, sub position plays a HUGE role in the frequency response you'll get at your listenting position due to differences in boundary gain, position relative to peaks and nulls, etc. The same goes with speaker positioning.
In your case, you have very little space. IMO, it is more important to keep some distance between the speakers and the sidewall - even though they'll be awfully close together in relation to the seating distance. If you can, I'd try a compromise. Move the mains a little further apart and move the subs closer to the listening position. Optionally, you can actually put the mains IN FRONT OF the subs and have the subs along the front wall. In either case, also experiment with getting the subs up off the floor.
The LAST place you want a sub is in the corner - contrary to popular belief. While it will produce the LOUDEST bass (due to SBIR and also the fact that it will excite EVERY room mode), it will never produce the smoothest frequency response and deepest extension.
If your options are only the 3 listed, then here is my recommended option.
Mains close to TV and subs by the side walls. Breathing room for speakers on the sides (less SBIR issues). Subs not in corner. In this (or any case in this room), you're going to need to address the first reflection points at a minimum and should also consider some broadband bass absorbtion.