The following VBA example creates two overlapping rectangles with uniform fills. It then enables separations, specifies the PreseveOverprints property as True, and prints the document.
Sub Test()
Dim s As Shape
Dim doc As Document
Set doc = CreateDocument
With doc
Set s = .ActiveLayer.CreateRectangle(2.110157, 9.605512, 5.69315, 6.94315, 0, 0, 0, 0)
s.Fill.UniformColor.CMYKAssign 100, 0, 0, 0
s.Outline.Type = cdrNoOutline
Set s = .ActiveLayer.CreateRectangle(3.428898, 8.859055, 7.111417, 5.89811, 0, 0, 0, 0)
s.Fill.UniformColor.CMYKAssign 0, 100, 0, 0
s.Outline.Width = 0.33333
s.Outline.Color.CMYKAssign 0, 100, 0, 0
s.OverprintOutline = True
With .PrintSettings.Separations
.PreserveOverprints = True
.Enabled = True
End With
.PrintOut
End With
End Sub