Editing registry entries isn't a friendly environment to learn but I'll outline what i did.
I'm using EmergeDesktop a Windows Shell replacement. I wanted to pass the command line argument 'hide' to emerge.exe when it was loaded as shell. Looking through the documentation i found where the registry entries where kept and what they were.
CMD > regedit. HKEY_CURRENT_USER > Software > EmergeDesktop
right clicked the entry i wanted to modify, clicked modify, entered the argument.
rebooted to make sure it worked.
FB