I am having difficulties distinguishing when the "Er" should be Do or Is...do you just have to know to get the sentence right ahead of time?
Er always means "is", but in English "agree" is a verb, whereas in Danish here enig is an adjective and "er" is used to say that you are in that state
This is exactly like in French "je suis d'accord" or Spanish "Estoy de acuerdo".
Becuase that isn't proper English. You would either say "are you im agreement" or more likely "do you agree".
I get the feeling that "enig" is equivalent to "one-ly" in english (though such a word doesn't technically exist.) It probably means "of one opinion" or something like that, in a more literal sense. Because that's more or less what agreement is, coming to a single conclusion amongst multiple people.