no it works fine with either, you just need to make sure you shut down epsxe correctly. you can do it by the file>exit method or the way squall mentioned, i usually suggest the file>exit method though because some people who are not well versed with epsxe are not even aware of what or where the log window is.
they should show up on both, playing from the disc or an image should not have any effect on that sort of thing. the way you exit out of the emulator only effects if the data is retained or not upon closing out of epsxe and when you start it back up again. do file>run BIOS and make sure your saves are showing up in the memory card manager, also make sure your memory card save locations are configured in the emulator's config as well.
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