Important limitation in Enterprise Portal deployment

You cannot out of the box run multiple EP sites, with different versions of User Control code, on the same IIS.

This is because SharePoint expects the code to be under the %System drive%:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\LAYOUTS\ep folder and you cannot deploy to different folders.

A workaround where you map the layout folder differently for each site, is described in KB944105. But it has some conequences, which you can read more about in the knowledgebase article.