I’m sure someone else will offer a solution but this will work.
If you haven’t already done this, make each circle and individual layer in Illustrator, import as comp into AE. Complete the movement of all circles & name this comp Base.
Now if you have 6 circles, make 5 copies of the comp “base”. Base 1, Base 2, Base 3….
Open Base 1, change the top circle to stencil alpha.
Next open base 2, turn off the top layer, change layer 2 into a stencil alpha. On base 3, turn off layers 1 & 2, change layer 3 into a stencil alpha. Repeat for the 5 base copies.
Create final comp, bring in the 5 copies, put your original as the lowest layer(6). For the five copies add the effect “fill” and select the color black. Now on all intersections, the circles turn to black.
Johnny Cuevas, Editor
http://www.ckandco.net