I don't quite know what you mean by 'level' the planes but the solution to your transparency turning black is that when dropped to the ground, a transparency needs to be raised by the smallest increment and it will return to normal.

Also,( and I can't tell from the above) it seems that you may be using grayscales for your transparency maps. You will always get a ghostly transparency if you do. Use solid black and white. Also, I wouldn't use layers because they blend. Instead, I would use mixed materials with the mix driven by another black and white image for the distribution. That will give you sharp clean edges. You can use layers for each of the mixed elements but only the 'mixed material' has a distribution function.

My 1.5 cents worth lol.......

M