To find the exact sizes of the circles, I think the best way to do it if you're just using a paper and pencil would be to just draw up the pattern real big, and then measure the radius of each circle with a ruler, being as exact as you can be. Then just divide the radius by the side length of the square, and you've got the circle radius relative to the square size.
In terms of finalizing the CP, it's really quite arbitrary; you pretty much just have to choose what circle sizes you want, and then just go with it.
I don't think my advice will be much help, but from my limited experience with circle-packing it's just a lot of trial and error

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Hi! It's been a long while since I've been active on here. I deleted my Dropbox years ago, so some things, like my Dragonfly Varileg guide, are lost to time. I may still have other things, though! Email me if you have any questions.