Program to start on start up, but run differently than if the user had opened the program

Question

Hi
 
I'm writing a program that gives the user the option to have it start on startup. I've managed to write some code that adds an entry into the registry, which runs the program. Is it possible to have the program run differently when opened by startup rather than by the user? e.g. when it opens with start up, it only opens to the system tray rather than displaying the form. Any hints / tips would be greatly appreciated!
 
Cameron