Sometimes, "pesce" can also colloquially refer to a fish dish, so perhaps the meaning is that the onion has been added to the fish. To answer Elena18's question, you could ask to the waiter "C'è cipolla nel pesce?" (is there onion in the fish dish?) if you wanted to eat fish but couldn't eat onion, and without implying the fish had been stuffed with it.
A couple of things:
First off - context. "in the plate" doesn't make sense. Translating is not just a case of manually exchanging one word for its English equivalent - if it were, a computer could do it perfectly and we'd just buy a babelfish if we were going to another country. But languages are not that simple.
"Nel" most commonly means "in the" but not always - you have to use your common sense to work out what it is likely to mean given the context of the rest of the sentence
Prepositions in Italian do not map one-to-one with the equivalent English preposition. For example "al" means "to the" more often than not... but in the case of "biscotto al cioccolato" it means "cookies with chocolate". Similarly "di" normally means "with", but not always
Because preposition usage varies from language to language, you can learn the general rules (ie. in = in, di = with, su = on, a = to), but you will always have to learn some idiosyncrasies as well. When you learn prepositions you have to think of it as "This one most commonly means ___ but not always. Sometimes I will have to use my common sense when translating"
Yeah, the root is Latin and I can't think of any English analogs.
Etimologia: ← lat. tardo cepŭlla(m), dim. del class. cēpa ‘cipolla’.
I do the same thing. I look for the root of a word. It makes memorization much easier if you have something with which to relate it. One tool I've found valuable is an app that's companion to Duolingo. It's called Tiny Cards. It has units that are made to go with the lessons. You can flash vocabulary and get XP in Duo. I devour vocab very quickly with it's help.