Change virtual directory?

I have a few websites hosted on a 2008 server with url rewriting
I have each site in a folder:
Site 1/
Site 2/
...
I hide the folder using url rewriting so that the address is http://site1.com as allosed to http://site1.com/Site 1/
My problem is, when I link to a file for example:
<a href="default.aspx">Home</a>
the url resolves to:
http://site1.com/Site 1/default.aspx
not
http://site1.com/default.aspx
Is there a setting that allows me to change the folder that the site thinks it's in?  Like a virtual directory or something?
Thanks in advance.
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