Not a teacher.
I don't know all the rules for pronunciation, but questions usually end with a slightly higher intonation:
How do you feel?
Who did you say went home?
Both of these rise in intonation slightly as the sentence goes on, with "feel" and "home" being highest.
Your other question does not follow this "rule":
Is the intonation up or down?
If I asked this question, I would rise in intonation until the word "up" and then I would lower my intonation for "or down." I don't know why, it just sounds more natural for me.