Visual Studio 2005 Team Edition, C#

Couldn't exactly decide where to put this, hope this is okay. From what I have seen, in order to use click-once the application must be installed via a click-once installer. Even if everything has been setup for click-once, installing via the MSI seems to leave behind the auto-update bootstrap.

I understand that installing via click-once is comparable to running the app in a sandbox, ect ect. What I would like to do, is have the user install the application via MSI (so that I may make registry changes and the like... just for the sake of argument assume that I must install via MSI). But I would like to leverage the auto-update functionality of click-once. Is there any way to combine the two?