So with this sentence..
"Wonen de jongens daar?" you are asking if the boys live THERE (as opposed to someWHERE else) because 'Daar' carries emphasis.
"Wonen de jongens er?" you are asking if THE BOYS (as opposed to someBODY else) live there. Because 'Er' doesn't carry emphasis?
If that made sense, can somebody clarify that I have the right end of the stick?
Yeah think you can say it like that in your example.
I'd say you generally use 'er' if it is clear what location you are referring to. E.g. in your example, you are not going to ask if the boys live there opposed to somebody else if you don't know the location. So there is some context involved when using 'er' when asking a question.
If you say: 'Zijn de jongens er?'. You could be asking 'Are the boys here?', for example if you know that the boys are or should be coming. But if the boys are visiting somewhere and you call there to see if they are there 'Are the boys there?. You can also say 'Zijn de jongens er?'.
So in other words, when using 'daar' you are pinpointing to a specific location in these examples, when using 'er' there is some knowledge on the location.
I answered: Do boys live there.? It marked me wrong, Why?? What does daar mean then?