It was my understanding that the continued subsidy for 3 years applied only to the remaining subsidized loan interest that was not paid by the borrower as it was accruing. I was not aware that you could circumvent the rule by applying a payment to the unsubsidized interest instead.
So my understanding is that if your subsidized loan accrues $1000 in a year, your unsubsidized loan accrues $2500 a year, and you write them a check for $1000, the $1000 goes to your subsidized loan interest; and the first of 3 years incurs no extra handout.
When you apply for IBR your loan servicer sends you a payment plan for each loan. If we say your repayment about $500 or so per year, which is about what most residents would pay (somewhere b/t $300-$500, though the OP's $0, which you can get if you're married and have 5 kids, etc), then that $500 will be split proportionately between all the federal loans, so that if you were to stay in IBR your whole life, the loans would all get paid off at the same time.
So while yes, your payment is applied first towards the accruing interest and then if you pay enough on top of that, then to the principle, it's applied to every loan's interest. So with your example, if you pay $1000 over the year on a total of $3500 in interest that accrued, then a little over a third would pay of the subsidized interest and the other two thirds or so to unsubsidized interest. That is my understanding from the IBR paperwork/payback plan I just received back from FedLoan--I will make only one monthly payment, but it specifies that $26 goes to this loan and $50 to this bigger loan, etc.
Since the OP is not required to make a payment, any payment he/she does make is an extra payment. He/she can specify which loan they want their extra payment applied to (FYI--you will need to specify if you want that payment to go to a particular loan). It that case, most of us would probably want to pay off private loans, GradPlus, unsubsidized Stafford, subsidized Stafford, in that order, since as the OP mentioned, the gov't will pick up the tab on the unpaid interest for the subsidized loans for three years while in repayment.
