Hi Tyrone
I can tell by the way you ask your questions you've got a good grip on understanding this project.
Make sure you use sand mix for the top layer, and try not to talk to any of the Home Depot staff while looking for it.
When I build my top layer of mortar bed in relation to the drain ... I always make sure that I screw the drain all the way out before I begin, and then turn it in as far as I think it should go to give the threads a good grip .... and then I keep turning a little bit more (about 1-1/2 turns). The extra turns will allow me to build my mortar bed using the top of the drain plate as a guide without having to take extra care with how low or how high I build my mortar bed. I scape everything flat and sloped as needed, and then turn my drain back out the 1-1/2 turns to accomodate the thickness of the mosaic tile.
When you spread thinset you will most likely force some in toward the drain and that's fine. Also, when you grout, some will also be forced toward the drain assembly .. so by the time you're done, it's solid in place.
The top of the drain plate should be flush with your tile ... maybe down only enough not to feel the edge of the drain cover.
Cut tile pieces from the bottom & grout the imperfections, if any, perhaps??
I'll tell you what I tell my helpers. "If you take your time there won't be any imperfections".
