Flooring Tile - Shower tile confusion

I had a contractor hired to create a shower (4' x 5') on a concrete slab and he gave me a list of materials to get. As he told me the items he told me what they were for. He repeatadly said that I could do the job myself after he had seen the amount of work I had done by myself thus far (a 28' x 36' addition).
OK so far. Since then he broken his arm and is unable to do the job and I am under the gun to complete this by myself soon.

My question lies after I poured the concrete base (on the poly boot with 3/4" drop to the drain in 3' span) "somewhat" even (affording several small dips in the consistency), what do I use to secure the upcoming tile? He had me get a goodsized bag of Latex Modified Thinset Mortar of which I used on the Durarock seams with fiberglass tape and also three 1 gallon cans of Premium Ceramic Tile Adhesive for walls and floors. Do I attempt to even or "level" those dips with the Thinset - then go to the adhesive? Or what ?

Thanks so much