(Czy) jest dobrze czy nie?
that's an example (somehow neglected so far in this thread) that the word "czy" can be skipped (quite often, in fact) and the sentence looks like an affirmative statement, but the question is represented by the question mark (in written) and by the intonation (in speech), for example:
Byłeś w szkole. - You were at school.
Byłeś w szkole? - Have you been at school? [Were you at school?]
Czy byłeś w szkole? - Have you been at school? [Were you at school?]
in composed sentences the "czy" has to appear:
Spytałem nauczycielkę, czy byłeś w szkole. (I asked your teacher whether/if
you had been at school)