I know Preps 6 only works with PDF's, not sure about Preps 7. I highly doubt they would add the ability to place eps files back in after they have switched to a PDF imposition.
If you switch to a pdf to pdf workflow. Plan on testing, testing, testing. Not sure if you print separations out of Preps to control which colors are printing, we did. But I believe we lost that control when we switched to PDF. We ended up controlling the colors in the Nexus workflow.
Do you have the PDF part of Nexus, which I believe is called TotalRIP?