How to use IIS 6.0 + Helicon ISAPI Rewrite 3 with multiple sites?

I am running an Windows 2003 box with IIS 6.0 installed on it. I am serving numerous sites on the box, which are placed in various folders within the Inetpub directory on the machine. All traffic is routed through the host headers set up in II6.

I am attempting to create all of my rewrite rules in the single httpd.conf filed located inside of my Helicon folder in my Program Files.

I am running into some issues when attempting to create rules for multiple site, as it seems the rules are being carried over from site to site from the single file.

Is there a better way to manage this?