When you breed 2 unicorns, and one of them has custom skin, then will the customskin be affect to the filly's skin?

Custom skins do not carry on when bred. That would make it very hard to generate art. The skin that the child will have will be based off of the parents genes (which you can see on their genetic chart). If you are confused as to which image this would produce please see the custom skin list: http://beastkeeper.com/skin-lib

If you have furthur questions I wouljd be happy to help with them!