if you create a new project using the "New WSDL Project" option , it will be added to the workspace.. alternatively you can import an existing project into the workspace with the "Import Project" option..
cant you have 1 project file for each client? And in this project all the clients interfaces? Projects are self-contained and can safely be distributed without any dependencies to other projects.. so you would give project 1 to client 1 and project 2 to client 2 !? Or maybe I am misunderstanding?