I'd recommend copying over the entire installation (ie the folder that contains the bin32, bin64, etc folders), to make sure nothing is missing wherever you decide to work.
To edit, copy the whole installation from the USB to the desktop, then run the Editor.exe contained in the CryEngine folder that's now on the desktop. (Putting it on the desktop will make it load faster.)
After editing, save as "Global", close the editor, then copy the whole installation back off the desktop and put it onto the USB again.