running multiple sites from one instalation of CI on Media Temple

[eluser]Yorkshire Pudding[/eluser]
I have looked at lots of post and I suppose it is more of a media temple question really. I suppose I just hoped someone else had a similar setup on media temple and could give me a few pointers. Basically where/how i could set up the system and application folder outside of the other virtual domain folders. Would it be a case of me in logging as the root and using putty to upload files (I've only used the command line a few times to make a couple of changes but would happily give it a go).

in other words I need to know how to set this up.

/system/ // <--- this system folders shared by all sites
/application/
/site1/ // <--- the application for www.site1.com
/site2/ //<--- the application for www.site2.com
/www/
/site1.com
/site2.com

If anyone can give me a hint or point me the right direction would be greatly appreciated.