ClickOnce applications are stored in C:\Documents and Settings\*\Local Settings\Apps\2.0\
(on XP. I'm sure you can figure out where from this on Vista, or whatever you're using.). Furthermore, each deployment version is stored in a different place, making this a rather interesting problem.
The way I did auto-start on my ClickOnce application was that every time it starts up, it checks the autostart registry setting, if it exists, then it sets it to the location of the currently executing executable, to be sure that the most current version is being auto-started (it handled updates manually and restarted itself when it was done).
If this is going to be a regular scheduling, then you're going to have troubles. If it's a once-off, then perhaps searching through the app cache might yield results. If you want regular scheduling though, I think you're going to find it will be infinitely easier to use a different distribution mechanism.