Plywood floor decking is designed to be supported at 24" spans, so if you're just gluing neoprene to the bottom of plywood panels, keep them 24" on center, horizontally and vertically.
Haven't heard this idea mentioned before... I don't know if there's any inherent problems with it. Certainly would save headroom... It'd be tricky to stand walls up on top of it, though; nailing them down around the edge would be risky. Perhaps you could put a bottom plate around the edge of the floor panel, screwed or nailed up thru the bottom, before you laid down the deck. Then you could just tilt the walls up onto that extra bottom plate. But that'd be as much or more of a hassle than just raising the whole floor up on 2x4s....
... just thinking out loud...
If you're supporing the floor deck on joists, 36" will probably be fine, because the joists can span a lot farther than the deck. If the neoprene is thin enough, and you space it out too far, the joists might deflect just enough to touch the concrete between the pads, but that's the kind of thing that'd happen if you spaced the pads 7 or 8 feet apart or more.
It basically depends on the joists you're using. Most of the advice on floating floors that I've seen talks about using 2x4s laid flat, and screwing the deck down to that. Since 2x4s laid flat won't span very far, I'd say 36" would be the very most I'd let them span. I also think that at that span, they'd be fine. Other people may correct me if I'm wrong.
Out of curiosity, is there any advantage to having a floating floor built off of anything taller/deeper than 2x4's laid flat? I mean, it seems like a waste of headroom to me. You could build it off of 2x6s on their edges (like normal floor joists) but why bother, when they'll only be spanning 2 or 3 feet between neoprene pads? If it's built over a concrete slab, then having a greater depth between the floating floor and the concrete (making a greater cavity between the 2) wouldn't help isolation any, would it? I'd think the greater value would be in preserving headroom inside the space...
Again, just thinking out loud.
Kase
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