Setting up an App to run hidden

Trying to find a way to have an application start and remain hidden (IE not show up on start bar, to the right of the start icon)
heres the situation:
we were using an remote control software called Proxy by Funk software it will launch prior to user loging on to network and remain hidden.
we are now using Desktop Delivery (DD manager) by AD-Spec and has to be manualy started by user i have put it in start up folder w/minimized.
is there any way (in the reg) to get it to start and is there any way to have it not show up on the start bar.

thanks Jim