Oh, you're doing the Plant-A-Sim scenario! I haven't tried this scenario yet but here are general tips on fertilizing.
I'm sure you know this already but there are three grades of fertilizer:
(1) Very best: Fish or plants worth $50 or more
(2) 2nd best: Fish or plants worth $25 to $49
(3) All the rest
So, if you have a normal lily worth $52 (forgot the actual amount) and a normal growfruit worth $35, you should use your lily as fertilizer until your growfruit is worth $50 or more.
Good luck!
You could also buy your sim a Chemical Analyzer to "Analyze Flora," which sometimes results in a quality boost. Plant, harvest, fertilize, Analyze Flora, rinse and repeat.