If you can decompose your circles into two groups (evens and odds), such that there is no overlap among circles within a group, the following sequence should give the desired effect:
- Clear the background
- Draw the evens with an alpha of 1.0 (opaque)
- Draw the odds with an alpha of 1.0 (opaque)
- Draw the evens with an alpha of 0.5
Places which are covered by neither evens nor odds will show the background. Those which are covered only by evens will show the evens at 100% opacity. Those covered by odds will show the odds with 100% opacity. Those covered by both will show a 50% blend.
There are other approaches one can use to try to blend three or more sets of objects, but doing it "precisely" is complicated. An alternative approach if one has three or more images that should be blended uniformly according to their alpha channel is to repeatedly draw all of the images while the global alpha decays from 1 to 0 (note that the aforementioned procedure actually does that, but it's numerically precise when there are only two images). Numerical rounding issues limit the precision of this technique, but even doing two or three passes may substantially reduce the severity of ordering-caused visual artifacts while using fewer steps than would be required for precise blending.
Incidentally, if the pattern of blending is fixed, it may be possible to speed up rendering enormously by drawing the evens and odds on separate canvases not as circles, but as opaque rectangles, and subtracting from the alpha channel of one of the canvases the contents of a a fixed "cookie-cutter" canvas or fill pattern. If one properly computes the contents of cookie-cutter canvases, this approach may be used for more than two sets of canvases. Determining the contents of the cookie-cutter canvases may be somewhat slow, but it only needs to be done once.