InDesign 2.0 and later is capable of outputting PDF 1.4 (native transparency) and PDF 1.5 (layers), both of which Prinergy handles well.

• Native transparency can be useful because of its increased quality and smaller files. Enable Native transparency in the Export PDF dialog box by selecting Compatibility: Acrobat 5 (PDF 1.4). Alternately, selecting PDF/X-4 from the Standard list in the Export PDF dialog is another good starting point for creating good PDFs for Prinergy's use. Check the other panels in the dialog box to ensure that other settings are appropriate for your environment.
• Layers are useful only if you are preparing files for use with Layered PDF Versioning jobs. Enable layers in the Export PDF dialog box by selecting Compatibility: Acrobat 6 (PDF 1.5), and then selecting the Create Acrobat Layers check box.

These settings can be saved as a preset in InDesign. For more information, consult the InDesign online help.
For more information about transparency, see About transparency support.