Run the program. You should start out with Download highlighted at the top. Put in your Lemmy instance and credentials where it asks. Hit the Download button, which will download a JSON file - it’ll pull stuff like subscriptions from your Lemmy account. At the top, tab over to Upload. Put in the new instance and credentials, and hit Upload. It should pull the JSON file it created when you downloaded and “set up” your new account you’re migrating to. You’ll still need to go in and adjust some things, but your subscriptions (for example) should be there.
EDIT: To clarify, Download is for downloading your “old” account info, and Upload is for uploading that info to your “new” account.