I would suggest the easiest method of doing what you want and ensuring that any already-existing recording is not overwritten is to save your project before you add any new elements (using an easily-remembered name). Once you are happy with the "new" recording and how it works with the older one, again save it but choose a different name again.
Thus, ALL your recorded tracks are safely preserved and, in the worst case scenario, e.g. the new recording simply does not "fit", the original recording can be reinstated simply by opening its project file.
1. Export the MIDI objects to MIDI files. This is done in the piano roll (MIDI Editor).
2. Music Maker does not have punch in/out, so you are best to use 2 tracks for recording multiple pieces. You'll want to start recording earlier than playing, monitoring the previous recording and/or metronome, then start playing at the correct location. Recording 1, 3, 5 on track 1 then 2, 4, 6 on track 2. Once you have adjusted the MIDI recordings (quantize, etc. ) then you can trim them and move them onto 1 track. Or, you can extend out the first MIDI object, and then copy/paste from other objects to one main one, or something like that.
3. You may want to look at recording directly into the MIDI piano roll by checking Overdub. I am having trouble as I start recording after the first part ends and the new notes go to 2 places, crammed up at the beginning and ok where they are supposed to be. More testing required.
Remember that the beginning of the yellow range bar is where recording will start.