I'm not really quite sure what you're asking.
If you want to play more than one note at the same time, you match up the Chord1 and Chord2 lines with the Melody line so it plays at the same time.
For example, if I want to compose this:
...I would put this in the Melody line:

cdefgab>c
...and this in the Chord1 line:

efgab>cde
It's easier to compose if you view your composition visually. You can use the MML editors (3ML Editor and Maki-Mabi's Sequencer), midi editors, physically write notes on staff sheets and sequence it on the computer, etc.