5
Templates are stored in the database. This is why you need to update the module after ftp'ing a changed template - this updates the database version.
If you have cloned the template set then you should only need to upload the changed file through the template manager, or edit it directly within the template manager... is that what is not working for you?
An extra pointer:
Make sure that admin->preferences 'update html templates...' is set to yes. This will update cached templates, if the template has changed.