I assume you are adding a layer of subfloor material to an existing layer?
Here's a crash-course in tile prep and subfloor management.
This top layer should be exterior grade plywood only and you only nail it to the first layer, NOT INTO THE JOISTS. The nails should be galvanized and only long enough to penetrate both layers of plywood. The seams must be staggered from the first seams and the end seams SHOULD NOT meet on floor joists. In fact, the long side should oppose the floor joists.
The nails should be around every four to six inches on the perimeters of the boards and six to eight inches in the field of the boards.
DO NOT fill the edge-gaps with anything solid. This subfloor must have room to expand when it gets ready to.
Same goes for the cement backerboard, don't nail it into the joists. The backerboard MUST be set into a fresh bed of unmodified thinset. The backboard seams also must be taped with alkali resistant fiberglas tape but wait to do this until you are ready to install the tile at the same time.
There should be a 1/4" gap on the perimeter of both the backerboard and the tile. A modified thinset can be used to install the tile but please please please don't use a pre-mixed thinset for any reason, I don't care what the guy at the Big Box says.