Link multiple pages with footer?

Just let me preface this by saying thank you for a great product. I am really enjoying all that can be done with Piwik.

I have just setup Piwik for a client that is a webhost. So today I added 40 websites each with there own user to log into and that all works fine. Seeing as that there is 40 sites all with multiple pages. I am trying to figure out the best way to get stats for every page per site with out having to add the tracking code one by one.
I know this can be done by way of a footer, but I have not been able to find much info on how its actually done.

The server that it is running on is Windows 2003 with IIS. I know i can add a footer html file to be added to all server requests per site, but it never seems to work.

The last thing that I tried was to make a piwik.js and put it in the website folder then make a html page that called the piwik.js and added that for the site footer via IIS. To me that seems like it should have worked, but it did not. If anyone can recommend a solution it would be much appreciated.