I usually start with all volume settings centered (which is the default) and if I have to modify I'd do so by reducing volume of certain vocals/instruments (not increasing any above center). This usually provides the ability to smooth out transitions a lot better, and I only increase above center if it seems necessary. Most of the MMJ samples are very clear, so you usually don't have to have too much volume. If you introduce your own recordings/samples, then you may need to turn those up.

For transitions I typically do it by quarter - so imagine from center to bottom of the volume control as divided into four even sections. I would jump up or down by section (quarter), and depending on how many cycles you have per instrument (1, 2, 4, 8) the transition can seem pretty smooth. When I use an instrument with a single cycle, I need to duplicate the instrument more to achieve the same play duration as a multi-cycle instrument, but it allows you to control the volume more granular at each cycle. Hopefully I'm not confusing you with the terminology, as I'm fairly new to MMJ as well.

As far as ending songs, I find using the above volume control approach, while also reducing the number of instruments along the way (down to one instrument) and a lower volume works well. You can also change it up and play with the scale, each iteration doesn't have to sound exactly the same, and often your tunes will sound more authentic (organic?) if you change up the scale (meaning the letters - a A# C, d, e, f) throughout the track and towards the end. Works well for EDM type tracks, but I imagine it can be used in other genres.