The document root of apache is set to be /var/www/vhosts/sitename/
The workspace in eclipse is set to be /var/www/vhosts/sitename/path/to/themes/folder/themename
That way I can edit things in eclipse and as I save them the changes are live on my local machine. If I make a new release [tag] in SVN then it updates [with rsync] my themes folder on my site.
[I use wordpress so dont need to keep the code for that in my own repo.]
This svn for web development setup can scale to work with many projects, and can work with many sites.