We have several deployments of the same assemblies with different configuration files for different environments. We package these up in to separate ClickOnce deployments with d
Try using MageUI. Open your deployment manifest (the one with the .application extension). Select "Name" from the list on the left and edit the "Name" textbox. Then select "Description" from the list and edit the "Product" field. That way you'll be able to distinguish your different installs on the start menu and in add/remove programs.
Save your changes, re-sign the manifest, and you should be good to go.