(---still in Studio 2011---)
When creating a project based on a template, you have an option to update the template at the end of the wizard (see screenshot, in red).
This option seems not to work... so that:
either you have to enter modification direct in your template (File -> Setup -> Project Template...)
or you must save as a new template at the end of the wizard (see screenshot, in green) and overwrite the old one by selecting its file name.