can you write (encode) a 3 track magnetic stripe, which is wider than
a two track, with a two track writer? would it just leave one track
blank or do you have to have a two track magnetic stripe on the card
for a two track encoder and a three track magnetic stripe for a three
track encoder?

Normally, only Tracks 1 & 2 are encoded.

Track 3 was intended to record transactions but I believe that it has
fallen into disuse with the advent of on-line technology.