Parameters or Registry keys? Which is best to tell an application to do "something" at startup?

Okay, I’m designing this application.

At some step it needs to reset the computer, run at startup and do some work. But the problem is that i need to save some “flags” from the first run, so when running at startup the app will run based on those flags? Should i save the flag states in the registry or should i just give them as parameters in the startup shortcut?

Thanks!