You're right, there's still some mechanics that aren't yet explained.
One of these you might not have found yet is the mastery upgrade. Let's say you've discovered all 3 of the Sproutling's branching creatures. The Sproutling is now "mastered" and has a star on its item icon. If you then go to the Sproutling's details screen there will be a new upgrade that will permanently upgrade ALL other producers in the game. This works the same for storage and buff creatures. (Again, not explained in the game yet, I'll fix that)
Other than that, the solution to crafting a high-tier producer or buffer's item is to put your best storage creatures by your converter and provide them with essence and maybe even buff them. Then use the last slot next to your converter for your "target creature" that you're trying to farm.
Thanks for the feedback!