You can wash the squares and then they will shrink and stop the bleeding. hopefully they don't shrink much but it would put your minds at ease. As for the size of the squares that would depend on the size of them after the shrinkage has occured, if you prewash them and the size of the pattern on the squares. You can't really cut something off in there, it makes it harder to know what they are. So I would take the largest pattern, measure it and then make all my squares the same size.
Thats just my thoughts though. Good luck with your I spy!