That is very confusing, if you're on a real C64 and the program asked you to type in "E" it would be fine if you type C+Shift+E ?
just type e (press the e key)
C+Shift mode is cosmetic, it changes between normal mode and lower case mode.
In normal mode if you press E, character code whatever01 is sent and put into the screen.
In normal mode if you press SHIFT+E, character code whataver02 is sent and put into the screen.
If you are in normal mode character whatever01 is shown as E.
If you are in lower case mode character whatever01 is shown as e.
If you are in normal mode character whatever02 is shown as
─.
If you are in lower case mode character whatever02 is shown as E.
The change between normal and lower case mode is performed with C+Shift, but it is only cosmetic, it affects how things are shown in the screen, not what characters are introduced when you press keys in the keyboard.
PS: symbols are only illustrative.