I would use the new multi tenant feature of SharePoint 2010 to segregate your customers. This will allow them to have their own admin areas and will make it so they can't see eachothers data or users but the sites can run under the same web application.
Then to resolve your issue of seeing all of your tasks in a single list there is a few things you can do such as rollups, workflow, CQWP, or even powershell.