Generate single program with program stop between each setup is an option on the Indexing tab of the Stock Properties dialog.
This option combines the toolpaths of all Setups into a single Setup. This means that when simulating the toolpaths, the toolpaths from all Setups are displayed and a single NC program is created. This option must be set if you are using a Sub-spindle. If this option is deselected a separate NC file is created for each Setup.
If Generate single program with program stop between each setup is selected, FeatureCAM inserts a stop operation between each Setup. This enables the part to be flipped and machined on both sides within a single NC program. For a turn or turn/mill document, the stop operation is created if the Setups are on the same spindle and oriented opposite to each other. For a milling document, the Setups can be in any orientation.