How do we understand if sie means she or you or they
Lowercase sie is she and capital Sie is you (formal/respectful) and they. Use the verb conjugation (verb endings) to help.
Why use "einen" here, instead of "eine?" Doesn't the "en" ending indicate plural apples?
einen Apfel = masc. accusative sing. (The apple is the direct object.)
Plural accus. would be (einige) Äpfel.