I have an older Epson with the same sort of 35mm scanning set-up. On mine, the software produces a pre-scan with all the negs showing. You get the opportunity to check, or un-check a box with each to say whether you want any particular neg. scanned as final.
After the scanning is complete, each neg appears as a thumbnail with an opportunity to rename the file. Once done, you can save them all to a folder as individual files.
On mine, I found the software a bit clunky, hope it's improved by now.