So, currently, when you put a stackable item into your bag, the slot it goes into is determined by this order:
1. Partial stack
2. Special bag type, leftmost bag with empty slot, leftmost empty slot
3. Base inventory slot (ie no bag in it), leftmost empty slot
4. Leftmost bag with empty slot, leftmost empty slot
However, when crafting something (or using any menu which lists all or part of your inventory, eg feeding batterflies, donating items, filling your still), the order in which the game pulls items from your inventory is this:
1. First instance of stack from the left hand side of your inventory (in other words, it doesn't care whether it's in a bag or not)
This often leaves you with two or more partial stacks, because, when gathering, your partial stacks are to the right, not to the left. This can be particularly irksome when your bags are more or less full, and you have to hunt around your bags to merge stacks.
I would propose, at minimum, that automatic usage order be, at the very least, changed to pulling from the rightmost stack first, or, ideally, an almost exact reverse of the order it goes into bags:
1. Partial stack
2. Base inventory slot
3. Non-special bag type, rightmost bag, rightmost stack (eg if you have a spice rack, but your allspice has overflown into your other bags)
3. Special bag type, rightmost bag, rightmost stack