Plural is chłopcy, singular is chłopiec and sometimes chłopcem. I am sometimes using chłopiec and chłopcem incorrectly. Could you explain to me why ?
Is a question mark on the end all you need to change this from 'you are a boy' to 'are you a boy?'
Yes. You can add "Czy" at the beginning to make it clear it's a yes/no question, but it's not obligatory.
If it is singular than why isnt it "chłopiem"?
Well, the Instrumental of "chłopiec" is "chłopcem".