Some applications allow you to specify an overprint setting for a specific color. InDesign CS, CS2 cannot define a spot color to overprint by default (that is, via settings in the Swatches palette or the Ink Manager). However, you can set Fill and Stroke to overprint for selected objects or set text to overprint in the Paragraph Style palette.

By default, InDesign knocks out overlapping colors, except for black, which is set to overprint.

The Adobe Support Knowledge Base has some tips/workarounds for this situation. Click here to read more.