If you just want to tweak an existing template, then make a copy of it using ftp.
For example if you wanted to change the iphone template.
Make a copy of public_html/templates/mobile_iphone
and call it public_html/templates/my_mobile_iphone
Then you can modify the contents of that.
To get the website to use it go into Joomla admin backend.
components> Mobile joomla > settings
on the iphone tab there is a drop down for template name where you would assign my_mobile_iphone.
Hope that helps.
PS I changed the topic of this thread to make it easier to find using search.