Welcome to the site aparente
Hmm I see what you mean about Ctrl+E.. It seems that SC won't let you use any hotkeys that the program itself makes available for editing within the program (you can see the list of these in the Screenshot Captor menus).
Since these Screenshot Captor hotkeys are hardcoded, there is no easy way to make them available for binding to the hotkey for capturing.
May I suggest that Ctrl+E and basically any Ctrl+Letter key is probably not a great idea for using because its going to be commonly used in many programs and you don't want to use something so common?
Having said that, Screenshot Captor will soon be getting a new hotkey configuration dialog that will probably let you bind to Ctrl+E, so if you wait a month or so you'll probably be able to do what you want.