Either will work - it really depends on the individual room, and other factors such as the crossover frequency you use. Every room has good and bad spots for sub placement, so you might want to think about putting in jacks and wiring for a few different scenarios.
A front corner is the most typical location for a sub but it really depends on the room and the sub.
From my personal experience with new home pre-wiring:
1) Make sure they run either RG6 or shielded line level cable to your sub location. My builder ran regular speaker wire to the sub location. Not typically what you would want.
2) Make sure they are using a reasonable size speaker wire. My builder installed 22 gauge wire. Luckily I caught it early and got permission to run my own wire while it was still under construction. 16 gauge would be the minimum wire size especially for longer runs and 14 or even 12 would be even better.
3) Most builders want to run 5.1 or 7.1 speaker terminations in the ceiling for LCR & surrounds. Unless you are dead set on in-ceiling speakers, try to rethink that choice especially if you have high ceilings like many newer homes do. Ideally you want your surround speakers at around 6 feet above the floor. Put them on the side walls around that height if you can.
4) Unless you go in-ceiling, you probably don't really need the front channels prewired assuming your amp/receiver will also be in the front in a typical setup.
This link has a pretty good basic speaker placement guide. You can Google for tons more.
Is it possible to change the size of your room even by a few feet? You gave a size of 16' x 16' for your new ht room. IF I remember right, you should stay away from rooms with equal deminsions for acoustics?? Any of you experts feel free to chime in now to correct me. I realize that this was not the question that you asked, but it might be something to have a look into since your under new construction.........
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