I am seeing contradictory informations.. .some use drywall mud others say use exactly the same thin set you plan to use for your tiles.
You have two situations:
Cement board to cement board
- You use thinset with cement board tape (alkaline resistant)... not just "grey" drywall mesh tape.
- With a small gap I will push in the thinset with thee index finger into the gap. If there is no backing... I give it a few minutes to dry out.
- then add the cement board tape
- WHOA - this is where you forget everything you know about mudding and taping. You will now put the thinnest coat possible of the thinset. If done right it will almost come to the top of the mesh backer tape.
Cement board to drywall
- Given that you are using the drywall appropriately and it is no longer considered a wet area
- you install using cement board tape and your choice of thinset or joint compound.
- you will be using the same technique as above, not filling the mesh tape fully.
By not filling the mesh tape (or going over) this should provide the flatest surface possible and with small tile you may need to put less thinset in these areas to negate the slight bump or ridge. Also there are techniques to smooth this ridge when putting on the waterproofing over the cement board.
The correct way to "mud the joints" is going to be to use tile thinset and a fiberglass tape made for cement board. It's similar to the sticky fiberglass tape made for drywall, but its thicker and more abrasion resistant since the thinset has sand in it and can be vary abrasive.
Sample listing, but sold at most places that sell the cement board: