Upgrading themes is very simple. Themes, modules, the Form Tools API and the Form Tools Core script are all upgraded in the same way. Log into Form Tools (as an administrator) and to to your Settings » Main tab. There, click the "Check for Updates" button. That submits all relevant information about your installation - including your theme versions - to the Form Tools site. The upgrade script then determines what components, if any, have been updated and generates a custom zipfile containing whatever you want to upgrade.
The generated zipfiles mock the folder structure of your Form Tools installation exactly, and only contain the files you need to overwrite. So, to upgrade the files, just upload the entire root folder to your own server, overwriting the old files. Once this is completed, log back into Form Tools and go to the Settings » Themes page. There, click the "REFRESH THEME LIST" button. That will update the database with that latest theme versions.