I have 2 gear sets, 1 for craftsmanship and 1 for magic craftsmanship, and it really isn't difficult to figure out what to use on each recipe. Just see how difficult the recipe is in one set through 1-2 synths. If you pile on the correct stat you'll see a LOT more successes and especially high progress (consistently above 15% and close to 20% on standard synths). On the other hand if you're focusing on the wrong stat you will notice the increased difficulty and a lot less returns on progress.

Many items in this game are tiered so if you figure out what stat to use on an item, theres a really good chance that the rest of the same type of item use the same stat. For example, all wands use Magic Craftsmanship, all lumber uses Craftsmanship.

Figuring out what tool is more logical in making a particular item seems to be a decent hint too, and stacking on Craftsmanship if it's the mainhand tool while using Magic Craftsmanship for offhand. There seem to be some exceptions though but it's at least a place to start.