You want to export via the export dialog and not make pdfs via the print to pdf command. Print to PDF is dead as of Snow Leopard and shows no hopes of return. There is no merit in using a PPD to produce your pdf. You would want to get a .joboptions file if working with a commercial printer.
In general using Press Quality out of the chute in InDesign is good enough. If you have bleed you'll want to set that. I generally do everything with all image resolution and color conversions turned off. Some people prefer images to be downsampled, I prefer let the RIP do it.
Hey PB -
If you still want to use your PPDs and I understand why you might - Make a folder inside the Presets Folder of Indesign named PPDS - Put your PPDs in there and they should show up for you -