Users who want to switch to the Online build must use the Windows Control Panel to uninstall the old version; they can then start using the Online build (which will install itself the first time you launch the application).
You could simply install the software by hand on any system where someone will be running Main Boss.
However, this can only be done by someone with Windows Administrator privileges.
Alternatively, you could use Windows Server Manager to activage Windows Server Update Services.
Typically, you will have a customized web page for this purpose.
You may be able to re-use your existing web page with this new version of Click Once.