I might suggest screen shots for help in navigation. There is nothing more memorable than seeing the interactive display of Sample Manager and locating how to turn the lights off in the chamber. I am starting to build a standard operating procedure for our fresh instrument. Good luck in your endeavors.
I have some experience of this from the UK customers.
Concepts that are sometimes difficult: You dont need filenames any more. You don't need to "load channels" anymore. Every time you process the data you get a new result. You must use the same processing method for Stds and Samples to get results calculated.
I have found that I needed to spend quite some time explaining the sample set channels results result sets concepts and encouraging the users to work in Result Sets, even if they need to do manual processing. Also to explore the use of Sample Set Method Templates as this makes complex bracketing and Std use very easy.
There are also some differences in terminology and functionality for Overlays to watch out for. Empower does not have the OFFSET function beloved of ChemStation users and users a different way to offset overlays.
I have found the attached slide useful to walk though the different concepts of what you do up front and what you do every day..