The only way your employee can manage you is if you allow her to do so. By saying nothing and essentially obeying her directives, you are rewarding the behaviors you would like to prevent.
If you want this employee to stop acting as your manager, you need to start acting as her manager. Meeting in her office does not automatically imply that she is power hungry, but if you sense that this is part of her strategy, you should agree to the meeting and hold it in your office.
When her email has a controlling tone, call her on it and let her know she is not to send you directives, orders, or demands. And this business of tossing papers on your desk has to stop, too. Put an in-basket on your desk and tell her to place important paperwork in it.
If you are reluctant to take these kinds of actions, then be prepared for her to continue her unfriendly takeover of your job.
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