MM32 works by slaving even numbered magnets to odd numbered magnets.  It does not care if you adjust the odd numbered magnets first, and then apply MM32 to slave (automatically adjust) the even numbered magnets. Or if you just create the magnets, apply MM32, then start adjusting, it works either way.

Personally I prefer to apply MM32 before I start adjusting. That way I can see the both sides of the figure deform at once. What you see is what you get. Another advantage of applying MM32 first, is that the even numbered magnets will be hidden, and the odd numbered magnets made semi-transparent, thus giving you a better view of your figure. On the other hand, if you deform one side of the figure before applying MM32, you can compare the two sides, and have  a better idea how far you have changed it from the original.