Wade Wegner wrote a blog post about this a while back.
Running Multiple Websites in a Windows Azure Web Role
Keep in mind: Every role in a deployment must stay together - you can't deploy one role to one service and the other role to another service. If you want to do this: Separate your roles into separate deployments. Then you can publish them to different URLs.
I would recommend you create an instance for each web app. This would reduce the risk involved with deploying updates by de-coupling your product deployments.
EDIT: (stolen from Smarx, Windows Azure with Multiple Sites in One Role not transforming 2nd web.debug.config to web.config)
When you add another web role, you provide a physicalPath to point to what you want deployed, and all the SDK does is copy the files it finds at that path into your package. It doesn't do a build.
You should probably be doing a build and a publish of the web app you want to deploy, and then point the physicalDirectory at the output of that publish step. (Make sure the directory you're setting in physicalDirectory contains exactly what you want to have deployed to the cloud.)