I'm going to drain/replace the ATF on my wife's 16 CX-5. I'm not pulling the pan so I know I will not be replacing all of the fluid. How much should I anticipate replacing so I purchase enough up front.

 

Drained ATF amount is listed in the FSM as a variable range with the maximum specified as 5.1 quarts. So you'll need 6 quarts on hand, in order to be certain you'll have enough, even though the actual amount drained will most likely be less than 5.1. If you're able to replace exactly the same amount of fluid, at the same ambient temp, then you don't need to check the level. However, if there's any spillage refilling (or you just want to), then do the level check procedure, and adjust if necessary. Use only Mazda FZ fluid.

 

Always always always check your fluid and never go by what you removed as a way to refill your ATF fluid.
I also advise that you do a Pan filter and fluiod change instead of only fluid so you can see what is on the pan magnet as well what has settled on the bottom of the pan. Also you can inspect your valve body for varnish build up.

And you DO NOT NEED to refill with Mazda aft as long as the ATF fluid you use is compatible.
I really recommend Castrol over Mazda and have used it in my Mazda for over 30K miles with several oil analysis confirming that there is nothing wrong with my transmission as well the Castrol ATF I use.
If you drop the pan the most you should need is 5 quarts as long as the original fluid capacity was correct to start with. .

ASE

 

I can't talk for Mazda USA, but Castrol makes/supplies oil for Mazda Australia.