I have a setup with this, and it seems to fill the farm up nicely without any wastage.
For the fertiliser, it involves the use of 1 iron autarchic OR gate, 1 iron OR gate, 3 pipe wire and your usual: 1 wood pipe and 2 stone / cobblestone pipes. (I was low on resources when I made this, but it does the job with 100% efficiency so why change it to gold?)
This pipe has the Iron OR Gate attached, with
these settings. When it detects the multifarm with less than 25% fertiliser in it, it'll turn on the red pipe wire.
This pipe then recieves the signal, which
starts an energy pulser as soon as it recieves the red pipe signal, taking fertiliser out of the above enderchest.
I somehow lucked out, and the signal stays on long enough for it to send exactly 48 items. Note that 25% would be 16, so it fills the MultiFarm to EXACTLY 64, with no overflow!
Enjoy!