Can I use ClickOnce for an already deployed project?

Your initial deployment has to be through ClickOnce in order to apply updates through ClickOnce. You would have to deploy a "new" version of your app through a ClickOnce publish, then from there on you could apply updates. As far as the user machines are concerned that first version is a separate and new install of your app, so you would want to provide instructions to remove the app through Add or Remove Programs first, then do the ClickOnce install. But your first ClickOnce deployed version could just be the same app they already have.