For our current customer, we have both WCF and SOAP webservices we want to expose, however IIS does not allow these 2 different types to live under the same website.
Therefore, I would have to create one of the webservices in a non-default website.
I wanted to use the BizTalk Deployment Framework for this, to make deployment easy, and to make sure the webservices would always be deployed to the correct website.
After some research, I found out this can be done by adding the following line to the first property group in your .btdfproj file:

<IISMetabasePath>IIS://localhost/w3svc/2/Root</IISMetabasePath>

Here you only have to change the 2 to the ID of the website under which you want the webservice to run, which can be found by opening the advanced properties of the website in IIS Manager.