Nice drawing, you have done a lot of work on this.
The Arrange hierarchy for filled polygons starts with the first one filled being the highest with each one after it going down a step. To demonstrate this draw three circles in a line, then enclose them in a rectangle something like screen-shot 1. Select a color and fill the first circle, then the second, and then the third. Change the color and fill the rectangle. Now the first circle filled is level 1, the second is level 2, the third is level 3 and the rectangle is level 4. With the rectangle selected go to Arrange and click "Bring Forward". The rectangle moves up a level and covers the third circle. "Bring Forward" again covers the second circle, again and the third circle gets covered. At this point you can "Step Backward" and each circle will reappear in turn. The "Bring To Front" and "Send To Back" are the big steps that move the object all the way to the top or to the bottom of the pile.
I'm sure you noticed that if you start filling from the inside and work your way out you avoid hiding filled polygons as you work. Should you hide a filled polygon the best way to find it is to use the "partial object extents" fence. To do this, use the "Selection Arrow" and move it to the bottom right of the fill just inside and drag up and to the left. That will get you the ambiguity popup where the desired item can be selected, of course, if there is only one item inside the fence then that item will be selected without using the popup.
With this much repetitive work, I hope you are using the option key with drag for copying, for greater accuracy use the option drag with the gripper tool. With the Gripper tool, notice a "Distance" box appears in the data window after you start the drag where the exact move distance can be entered. It will do the same thing for rotate.
You might also find the "Select Mask" tool helpful for picking which type of objects get selected when drawing fences.
If I can be of any more assistance, just ask.