Is there something in this phrase that indicates "onion" is plural?
"I eat" should be accepted
How do you know if if bił is with or he/she/it?
Only the context, I assume
Is "chicken with onions" a common Navajo dish?
Nope, trust me lol
bił seems to be optional when using yishą́ in these lessons; at least I haven't seen any rhyme or reason to why/when to use it.
Bił means with, it is optional just like in English (I eat chicken, I eat chicken with onions)