No, there is no difference. In both cases the Polish translation is exactly the
same: "Jesz chleb". The context (of the situation or additional wording) will show if the talk is about the person eating bread now, or about his/her habit:
Jesz chleb - You eat bread/ You are eating bread
(Codziennie) Jesz chleb - You eat bread (every day)
(Teraz) Jesz chleb - You are eating bread (now)
In Polish questions, you may use "Czy" at the beginning (for a yes/no question), but you don't have to. Just putting a question mark at the end of the sentence instead of a dot is enough to change a declarative sentence into a question.
"Jesz kanapkę?" = Are you eating a sandwich?
"Jesz kanapkę." = You are eating a sandwich.
The two examples you've given for translating "jesz chleb" are You eat bread (habitually) and You are eating bread (now).
But You eat bread could also be telling someone to do it. Eg 4 kids.... David you go to your room, Paul, do your homework, John, eat this fruit, and you, You eat bread.
Would that final "You eat bread" also be "Jesz chleb!"