Hello,
In older versions, there was an option to do this, but in the current version (1.1.2) there is no such option anymore. Or at least, I can't find it.
FTP support is also in the 1.1.2 Version but it is only displayed if it is needed (different ftp and wwwrun user). So if you don't see the ftp support you should be able to edit all files with your wwwrun user permissions.
If a index.php from your template cannot be stored (changed), please check with your ftp client the permissions. Maybe the index.php ist set to noone (chmod 444).
Matthias