I would not ever flush-mount a sub. It limits your options way too much, even assuming that the optimal location happens to be at that spot in the front wall (as opposed to a few inches further out/in/up/to the side). I would also not ever position a sub on the room center-line, as that creates more problems that it solves. (For a start, it places the sub in a null for itself, for certain frequencies related to the room dimensions (especially width) and a peak for other frequencies...). There's also the issue of the sub itself: Some subs have downward-firing drivers or ports, or other physical design constraints, that make them unsuitable for flush mounting, or indeed for any type of "in-wall" mounting (flush or otherwise). A fixed mounting location for the sub also assumes that nothing in the room will ever change. If you decide to put in/take out racks of gear, move the client couch to a different spot, or take it out completely, or put one in when you didn't have any before, or replace it with a considerably larger/smaller one... any change to the room that modifies the location/mass/size of large objects in it, could potentially require moving the sub to compensate. This is a real issue: In the first of the two studios I'll mention below, we really did have to move the subs around aster the owner changed his main speakers for a different brand/model, and also after he move the client couch to a new location. It's not just theory: it is necessary in real life too.
Of course, with the above comments I'm assuming that you want a room that is accurate in the low end, and where mixes translate well. some people don't seem to care much about accuracy, or following the ITU BS.1116-3EBU / EBU Tech.3276 specifications for such rooms. It's a matter of personal preference, I guess. If acoustic accuracy and good mix translation are important to you, then it's a good idea to follow the best practices for achieving that. As Glenn mentioned, there are tried-and-tested methods for doing that, such as the one he outlined for sub placement. It just works, and there are solid, sound, technical reasons why that works. Here's the type of response you can get from a well designed and
properly treated and tuned control room: S3P. That one used two subs, one a little away from the front wall, slightly offset to the right, and the second one next to the far left leg of the left wing of the desk. Here's some similar graphs from a room that we are currently tuning, also with two subs, located inside the speaker soffits, on the floor, next to the side walls, but in different positions that were located using a similar method to what Glenn outlined:
Frequency response and phase response (full spectrum, 12 Hz to 22 kHz):
Low-end spectrogram (20 Hz to 230 Hz - the most important part of the spectrum):
RT-60 decay times in one-third octave bands (Full 1/3 spectrum, 45 Hz to 12 kHz.) The horizontal cursor line marks the original design goal for the room, at 200 ms. :
The same one-third octave decay times graph, but with the BS.1116-3 overlayThe highlighted section shows what the BS.1116-3 specification requires for critical listening rooms. The spec calls for the times in adjacent 1/3 bands between 200 Hz and 4kHz to be within 100ms of each other (+/-50 ms) This room is far better, with less than 86 ms difference (+/- 43ms).
In fact, the room meets the +/-50 ms specification over a far wider frequency range that the spec calls for: from nearly an entire octave lower (120 Hz) to 2 1/2 octaves higher (20 kHz, all the way to the top of the spectrum):
Low-end waterfall plot (20 Hz to 230 Hz - smoothed to 1/6 octave):
And because some people might think that smoothing such a graph is an attempt to "hide" stuff, here's the waterfall plot, with no smoothing at all (1/48, the lowest setting you can get on REW):
As you can see, both of these rooms get exceptional acoustic response, even better than is required by the specs for control rooms: Because they were designed, treated, and tuned using industry best practices, such as those mentioned by Glenn and myself earlier and in other threads. That's what can be achieved in a properly designed, treated and tuned room.
I doubt that it would be possible to achieve such results with a sub locked into a fixed location in the front wall, and inadequate bass trapping / overall treatment.
Sand-filled walls?
Well, color me skeptical on the cost/benefit for that, apart from the complexity, and not to mention the risks. Ditto regarding flush-mounting the rear-surround speakers. Here too, if those are in fixed locations, you cannot adjust them to meet the various different versions of 5.1 layout. You are locked into one single version, at that specific angle and elevation.
But having said all that, I go back to the point of how good you want your studio to be. This is is somewhat of a personal preference issue, depending on the purpose of the studio: If it is just for hobby mixing, making demos for your friends, or your own personal work, then accuracy need not be a big issue. If you want to do high-end pro work, and especially if you want to do mastering in there (either now, or in the future), then better precision and good translation would probably be important. On the other-other-OTHER hand: some "hobby" studio owners still want very high precision rooms, and some high-end pro studios seem to not care at all about such issues....
- Stuart -
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You have a pretty major investment in there, and I know all the heartbreaks, setbacks, problems, and delays that you've been through over the years it has taken you to get where you are today 
.... so I was rather certain you'd want to get is as good as it can possibly be.