Yes. Exactly the scenario I saw at two shop locally. They have a paper 'setup report' that the operator uses to set up the machine before a run. Part of it lists the tools and which slots (toolnumbers) to load them in to the ATC.
If a shop runs a small number of parts or parts of a very similar type, they probably run like herbk describes. But if they run a wide variety of parts/materials or specialized tools, then setting up the machine is job #1.