You could place your rectangles MCs on the stage by hand, make sure
each MC is named mc1, mc2, mc2. Then put references to the MCs into an
array, create a for loop that traces out the properties you're
interested in (x, y, rotation etc). Then you can move the rectangles
about by hand until your happy with the positioning. Then, take the
final trace values and update your APE code.
It's not very programattic, but it gets around the problem of updating
the APE code, compiling, damn out by three pixels, update, compile
again etc.
Hope that makes sense.