There is no nice function to achieve this yet. The following trick works more or less, though:
Use getref to search for a reference with the journal that you want to add a synonym to. If possible, use the reference that has the most information available for the journal (e.g. full name and custom abbreviation). Use the -o option to write the search result to a file.
Edit the temporary file and add the tags "JO - ", "JA - ", "J1 - ", and "J2 - " as needed. Save the file to disk.
Use the updateref command to change the information in the database, specifying the temporary file as the argument.