I have a feeling you meant to say the floor is not flat instead of not level. And you say it's off only 1/16"? Are you sure that's all?
We generally use leveling and patching products over the backer board not under them. As you know the boards need to be fastened, so Portland patches under the board is not a good idea.
Did you buy the thin set mortar to set the Hardie into yet? The special mesh tape, screws? Thin set for the tiles? What kind of tiles?
Jaz |