the gaps on the old plywood will be unaffected by the new plywood. The new plywood should have the same gaps all around the edges of each sheet. This allows for movement within the panel. (it will happen) not doing so will cause the panel to buckle and the floor to squeak. Also never line up the edges of the bottom and top sheets. You need to overlap the seams by at least 24" Glue and screw the two sheets together.
As a side note... there is no need to add this top plywood
As a side note... there is no need to add this top plywood