Hi Melody,
Patch things up with your husband because it's not that bad. The recommended amounts of thinset are for setting tile, which needs 100% coverage and a complete bond. Seating your Hardibacker isn't nearly so critical as your aim is to provide a consistant bed and eliminate possible voids between the CBU and the plywood. Unless you plan to do some table-dancing on this counter top (We don't need to know, actually
), any small voids left from inadequate thin-set coverage still won't be a problem. You want your top to be SOLID, and that's all. If it flexes when you put a load on it (which I doubt will happen with your double-layer of plywood) then you might consider re-installing the CBU after reinforcing the plywood.
In the future though, the CBU doesn't need to be beat on with a carpeted board. Simply comb out the thin-set and screw/nail the CBU in place. The pressure of the screws/nails will be all that you need to seat the CBU unless your thin-set is mixed too stiff.
Now get to work on that granite and send us some photos,
Shaughnn
My husband decided to be a sweetheart and help me, so that I could finish this granite countertop quicker. To make a long story short, I screwed and nailed down 2 3/4" pieces of plywod. My hubby mixed the Laticrete 2?? (good stuff), put it on top, then applied the backerboard on top. (He used a carpeted board to "pound" it down.... After 3 hours, he screwed down the CBU (HardiBoard). 
