I have Music Maker 16, so I hope this answer applies to your question.
First, in the program, press the "Y" button on yor computer keyboard. This will open the Program Settines dialog.
Now find that tab for Audio/MIDI, then near the bottom, there is a button that says "Arrangement Settings". You might be asked if you are sure you want to discard the current arrangement settings and open this dialog, if you say yes, in that dialog you can change the time signatures using the beat type portion of the dialog.
Please note that making this setting change will change all new projects opened, so if you want it changed to something else, you will need to go back into this area.
I think the samples are recorded in 4/4, you might need to create your own using things like the Vita... I am not sure if changing the time signature will alter the already created MIDI... that is something I will need to test.