Flooring Tile - Plywood repair before thinset and Wonderboard

I am wondering if there is any specific material that I need to use to patch my existing plywood before using Thinset and Wonderboard. We gouged a few areas when we were removing the vinyl and its underlayment. I also have an area where two pieces of plywood join that isn't exactly the same height. When I placed a piece of tile across that joint (just to see how much it was off), the tile rocked a bit. I don't want to have a tile crack later just because I needed to prepare my floor better. The Home Depot people told me that Thinset and the Wonderboard would be adequate, but I want to be sure. Can you help?

The thinset under the cement board will take care of these irregularities and provide a stable flat base for your tile.

Thank you!! I appreciate your response.

if still concerned about it you can take a belt sandewr or 6" angle grinder to sand down the crown before putting down the underlayment:cool: