A couple of observations on fertilizer:
-When your flowers turn brown, water them. IF after watering them they remain brown, they need fertilizer.

-When you go to the store to buy fertilizer, you will notice that the "type" will be highlighted. This seems to indicate the highest strength you currently need.

-When you have a flower that needs fertilizer, go ahead and "take" it (pick it up).
DO NOT FILL IN THE HOLE. Instead, go to your inventory and touch the flower.
(If you're still next to the hole, it will be replanted).
When you touch it in inventory, the name of the flower (I.e. Lemon Maranta) will be spelled out in different colored text indicating it's level of rarity.
*side note: this also applies to bugs and minerals*


I could be way off here, and if so hopefully some expert will step in and correct me. Still, this seems to fit my own personal observations and it's how I am doing it.