Herb bonus for trees.

No. It has to be right next to the item at the start of the day (or, when you put seeds in the farm for the well, or plant the herb patch, etc). Otherwise, no boost. For example, I planted my first bloody herb patch before the apple tree, and, despite the apple tree I planted right next to it, I only got five herbs, when the minimum with a boost is 6. At the same time, something like a furnace will get the boost automatically as long as the tree that boosts it is right next to the furnace. In other words, your herbs have to be touching the boosting trees at midnight, but you can move the furnace around so that you can be more or less likely to fail on refining to train it. (Because the furnace itself is not consumable, while herbs are)