Philandre,

If you say "yes" to transpose, any chords and notes you have already entered will be raised or lowered accordingly.

If you have not entered any notes or chords yet then it does not matter.

Saying "no" is useful if you want to correct a key signature. Say you entered chords for a tune in Eb, then you notice the key signature is still in C. In that case you would want to keep the chords as you entered them, so change the key signature to Eb and you say "no" to transpose.

Jim