Johnnycamp5, did you just put the sand on top of the speakers or under them? It's funny, it was an old thread about building a floating sandbox over a suspended wood floor that got me started on all this.
I'm often undecided about the volume level of the flanking subs. With the towers 4 or 5 feet from the wall the flanking subs get turned up more than they were with the towers 2 feet from the wall. Just enough to fill in the low end and not enough to muddy up the presentation.
As for blending the subs, a borrowed Crown XLS amp went in the system a while back but it just didn't blend well. It had a 4th order slope on it's built in crossover. It had about a week in the system but no matter what the settings were it just didn't sound quite right. Right now the system has a plate amp with a 2nd order slope that's much, much better. The sub in the back is a 4th order crossover and crossed over about 50 or 60 hz. It's seamless, too.
I've heard the 3 pi and the 4 pi's at the Lone Star Audio Fest several times and they sound great. Unfortunately my woodworking is terrible and the guy who build the 2 Pi Towers for me has since retired. For the time being it's fine - the 2 Pi's are sounding better than ever.
Wayne, the areas that aren't crawl space have a full basement under them and some additional wood reinforcement. There's also a ceiling attached to the basement rafters made of some moderately porous material. It wasn't put there to absorb sound but it does. The sound of that part of the room is probably the equivalent of the 2nd floor rooms you mentioned.
Playing around some more with thumping on the floor it's also noticeable that different areas over the crawl space are different. A few feet away from the wall is where the sound is a big thud with an echo. Yet right against the wall the floor is pretty solid. So in that part of the room the towers are either going to be 5 feet out (on the old foundation) or right against the wall.
It's a big deal. Most of the speakers that have been in the room over the years have never performed as well as expected. They all were positioned somewhere over the worst sounding part of the room.