As mentioned above you could (or should, some could argue) place your templates under mysite/templates/...
(especially if they are for the cms) if you have themes enabled (am pretty sure) SS looks into that theme folder first for templates which can sometime be annoying and create caching issues...
I personally don't use themes anymore, I just have everything under mysite
which I actually call something relevant to my project, keeps things tidy and easy to publish.
Note: themes are still useful, but maybe more for site that would change design, like e-commerce site with a xmass theme for example. I think there was a discussion about this on SilverScoop...