Not sure what the difference between the two are. In my software I 'm given themes which have their own individual css style sheets that determine the colour of the menu bar, buttons and I can upload, switch them whenever.
In my admin I have a templates section, with css coding to edit the homepage layout.
Lol, what's the difference between CSS and Templates?
Well..you can't code a site with CSS. CSS is just the presentation. The markup and page structure is done with HTML/XHTML.
So basically you design your site in your preferred software, then you create your markup and page structure with XHTML and then you use CSS to style it (position the different elements, colours, fonts etc.).
If you're using Wordpress I.E (I don't know if that's what you're using YesYouMay?), the templates are .PHP files containg the XHTML. So that you can chop up the different bits of your pages to be repeated. For example you could have header, footer, content, and sidebar. They are the templates. In Wordpress you can create a new content template containing your content area and sidebar for example if you want a particular page to have a different layout. Then you can assign a specific page to use that template.
All this together will make a theme. So you can create your own from scratch or use an existing theme like you're doing. So a theme is just templates with XHTML and PHP and then the CSS takes care of the presentation.