Originally Posted by Fallingwater
...All I want it to do is to rewrite the existing epubs with the margins I want, while leaving the files where they are. Can it be set up to behave like that?
No, as user_none stated, but...
...you can, after conversion, use the Save to Disk function to send the converted files to a single folder. You can use the associated drop down menu to select a single format (ePub in your case) or simple enter "epub" in the appropriate field in Settings to make the default button action to be ePub only.