Designing Kitchens and Bathrooms - Kitchen countertop using granite tile

I am in the process of remodeling my kitchen. All cabinets are in and I have the countertop base built out of 3/4" exterior plywood glued and screwed to the base cabinets. I then applied a layer of modified thin-set using a 1/4" x 1/4" notched trowel and laid on 1/2" Hardibacker board and screwed it down on 8" centers as was recommended in the instructions. All seemed well, I cut and dry fit the tile and bullnose edge pieces with no apparent problems. I started to install the tile on a small 2' x 2' section so that I could see how it would go together. I mixed up a batch of modified thin-set and applied it with the notched trowel. I placed the tile and was having trouble getting all the edges to match up close and level. No matter what I did it was not working. When I put a level on the surface I discovered a "crown" in the middle or the base surface. The same level indicates that the surface is flat and level from front to back and along the very front edge. Somehow I have a high spot in the middle. So, the question is - Can I (should I??) apply a light layer of thin set and trowel it smooth to level the surface or are there some other tricks that might help me do this job right? Of course I would let the leveling layer cure before applying the tile with another layer thin set. Thanks for any feedback or ultimate wisdoms.

This is why most folks will recommend 2 layers of plywood. Front to back the spacing is approx 24" with no support. Cement backerboard offers little to no structural strength. Its best to go with the two layers of plywood and the 1/4" cement board. If the substrate is stiff enough, no flex in it you could fill the low spot with thinset. If the substrate is flexing, you need to do something to correct that before you go any further.