There are two major reasons that a taxpayer must file all of his/her past due returns before the IRS will consider an Installment Agreement.
1. The IRS may owe you a refund for some of the years you did not file. And the refund can be used to offset the years that you may owe.
2. The IRS charges taxpayers a fee (around $105) to set up an Installment Agreement - so I would think you would want "all" past due taxes included in the Installment Agreement.