paydowns affect the non-aquisition debt first. That is true whether it is due to normal amortization from monthly payments or you decide to make a siginficant principle payment to paydown the debt.
but that is to your advantage,
the interest on the aquisition debt is tax deductible; the interest on the rest of the debt is not deductible. So you'd want to pay down the non-deductible debt first.
As I stated previously, taxing authorities really don't care if you take less of a deduction than you are entitied to - it saves the taxing authority money. So if you really wanted to paydown / payoff the aquisition debt first, which means less of the interest is tax deductible, the IRS is not going to care.... as the end result is you are paying more in tax than you are otherwise obligated to.
