yes, now that the cement board is up, patch the seams w/ thin-set, check your surfaces for plumbness and levelness, fix any out of wack areas w/ more mortar mixed stiff and use a wet, clean trowel to smooth it over. You can sand bumps and ridges after it dries. I would get a small bucket of waterproofing rubber and waterproof the tubdeck surface and up the walls 16" or so. Waterproof over the front edge to the floor if that is to be tiled also. Set your tiles w/ thin-set and take your time laying it out, tub decks are pretty wacky to lay out when you try to line up all the joints w/out having small cuts.
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Bradley