All I can tell you is that I use it with both my Sony PRS300 and Sony PRS600 - just NOT at the same time.
I think the issue for you will be choosing a "default" conversion format. Hopefully someone else can tell you which the best choice would be for both readers. Since they both read ePub, it's possible either format would work for either reader. You can read Sony ebooks on the Nook (although not vice versa because of eReader's specialized DRM).