Yeah, I have no idea on how to add programs to the quick launch..
(Right click --> Quick launch)
Im pretty sure there is a simple solution but i've only really been using Litestep for about a day >_
Edit $LiteStepDir$\profiles\$username$\personal\popup.rc and add Popup lines for each app you want to add.
or just go back to windows shell briefly and drag and drop the shortcuts into the tray from the desktop, its what I ended up doing for the same reason
I don't believe the QuickLaunch folder in the popup reads from there, although it could if configured that way.
The quicklaunch in Litestep's default popup is read from the following folder...
%USERPROFILE%\Application Data\Microsoft\Internet Explorer\Quick Launch
Just move shortcuts there. You can also run that path in a command to open the folder for you - which is the equivalent to running $quicklaunch$.