How do you input chord progressions for a song in music maker?

 If you are talking about chords from samples (not midi) when you pick the sample there is a row of buttons along the top area of the sample menu. There buttons (numbered 1 - 7 ) are the chord progressions for that sample. Drag one of those onto your track and you are good to go.

I assume you mean in a midi track - click on an empty track and select create new midi object and then select for example 'empty 4 bars', then double click this midi track and draw in your chords with the pen tool. you can then select which instrment you want to be played by the midi track