Just one period. You always leave off the period of the quotation, the same as if the it were not at the end of the surrounding sentence, but American usage pulls the sentence-ending period back inside the quotation mark, because it's prettier. It's really just a typographical convention, not really a grammatical one.

My opinion is that a footnote indicator should immediately follow whatever it's referring to, and it might be referring either to the quotation or the sentence, so I don't know that there's a single answer there. If you're footnoting the quotation, and it's at the end of the sentence, and you're putting the period outside the quotation, I would put the footnote indicator on the same vertical as the period, if possible. Otherwise, I'd put it after the period, as that gap that would be created between the end of the sentence and the period is awkward and ugly.