As stated in the FAQs, Craftmanship vs. Magic Craftmanship influence is per recipe.

Usually, I've found out that recipe where I only process the materials or assemble them, craftmanship will give me better results, while recipies where i transform the materials, magic craftmanship will be of greater help.

Example:

Fish cleaning a Maiden Carp = Craftmanship
Making Grilled Carp off Maiden Carp = Magic Craftmanship
Juices = craftmanship
Salads = craftmanship
cooking or baking = magic craftmanship
eic.

This also been proven working for me with my other crafts.

Give it a try, and let's compare results