I have a house poured on a concrete slab. I am tearing out the old ugly tile in the bathroom. In a few places where the nails where to hold down the carpet the concrete is coming up and leaving small craters basically to describe it. Is there any type of material or substance to use to fill in the small holes so i can lay new tile down. I am laying the tile that just sticks to the floor and i'm worried if i don't fill in the holes down the road it will cause problems, and since i'm starting from scratch I thought I better do it right the first time. Any suggestions would be great. Any other suggestions or tips on installing this type of tile would be great as well. Like should I use anything in between the seams of tile. to make sure they seal since it is a bathroom?

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?