rewrite and subfolders

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Our core CMS (Concrete5) is installed in the root directory, and has it's pretty urls enabled (url rewrite) so as to remove index.php etc..

It works fine, but now an additional CMS (Expression Engine) is installed in a subfolder (/site). The installation is complete but not accessible as you can't go to mydomain.com/site/index.php.

Is there anything you can suggest to make the two CMS' work? there is a .htaccess in the sites folder.

It's been mentioned to me about excluding the /site directory in the rewrite, but don't know what would work, and the best place to put it.

The code in the root .htaccess is:
suPHP_ConfigPath /home/catalyst
# -FrontPage-
IndexIgnore .htaccess */.??* *~ *# */HEADER* */README* */_vti*
<Limit GET POST>
order deny,allow
deny from all
allow from all
</Limit>
<Limit PUT DELETE>
order deny,allow
deny from all
</Limit>
AuthName catalystnetwork.org
AuthUserFile /home/catalyst/public_html/_vti_pvt/service.pwd
AuthGroupFile /home/catalyst/public_html/_vti_pvt/service.grp


Any help?