It sounds like you're asking about detecting watermarks when the stamp is still on the cover. There are several threads you can find by using the search function with different answers ranging from "nearly impossible" to suggesting different approaches that may help.
Here's one:
https://goscf.com/t/45526Could you show a scan or two so people know what stamps you are talking about?
Even when the stamps are off piece, I still have difficulty sometimes seeing the watermarks with watermark fluid and a black tray though I am getting better at it with time and practice.