Just did a 3/4 X 4" B cherry install last week. This wood is very hard and does not always slip together easily, I would not recomend building up specific areas, if you are going to put down a 1/4" ply, do the whole area. As for the different heights of the tile, put reducers in. They can be purchased where the flooring was, or you can make them out of the left over wood from the installation. Now, the staples, just hit them into the plywood with a hammer, as long as there is no padding or carpet stuck in the staple, you will be fine.
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