Dan, it'd be helpfull to know the brand of your machine.
On Haas mills:
For programming you just call up a tool as normal: M6 T1. No need to stage tools as the control looks ahead and stages them for you.
In MDI: Either type Tx and hit ATC Forward (or reverse). Or look at the pocket number of the tool you want and type Px and hit ATC Forward (or reverse).
The control keeps track of where each tool is so you don't have to.