You can set the toilet right on the subfloor with the wax ring if the flange is not so high it hits the bottom of the toilet when it is set in place. Set it just like it is on a finished floor. When I renovated my bath the last time, I set mine on the bare subfloor for the short time before the tile went down.
In regards to the shower and mentioned in another post, if you have a tub/shower combination, you can use poly to cover the walls for the time before the tile goes on. It needs to be set up in one piece with the lap at the shower head.
If you have a shower stall with a tile floor to go in, DO NOT use it. I am sure the soap deposits will do harm on the bonding of the tile to the lower part of the shower. Typically showers are used with tile in place, the tile sheds a LOT of the water to the drain. The mud bed, at least the way I seen them done, accept water readily including the soap dissolved in the water too. Yes there SHOULD be a pan under it all, and yes it should divert all the water to the drain. This is not the intended use for the shower. It needs to be used with all parts in place....