The refine process handles overprints and knockouts two ways:

Manually overprint or knock out colors by configuring the Overprint conversion options section in a Refine to PDF process template.

Set Colors to Knockout
Overrides the overprint setting in the input file and forces the colors to knock out. The order of the objects in the display list (that is, which object is on top) determines which separation knocks out.
Use this feature for disabling overprint and enabling content color matching for all objects on a PDF page.

In addition to these manual overprint settings Prinergy Evo also performs automatic overprint conversions.

Set Black to Overprint
Sets all pure black objects (that is K=100% and CMY=0) to overprint. Select the Set Black to Overprint check box to enable this feature. Clear the check box to disable this feature.
Regardless of whether or not you select the manual overprint conversion settings, the system performs some automatic overprint and knockout conversions on the following: