the problem with the translation into English is that is is grammatically clumsy at best;- I cannot imagine the context in which anyone would say "Have you gone yet?" whilst it acceptable (using English) to say"have you been yet?"
I thought "eto" was "yet." Now it's "again." Can it be used for both, and how can you tell the difference?
It is used for both. How you translate it depends on the context.
What's wrong with "Have you already gone?"
eto does not mean 'already'.