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Where will the payments be applied?

Any payments that are mandatory as part of the offer (eg, a periodic payment or initial payment), the IRS will apply the payments in its best interest: oldest periods with the shortest CSEDs first.
Taxpayers making voluntary payments are allowed to designate those payments in their best interest, hence Form 656, Section 5. Once the Offer is accepted, any payments after that would no longer be voluntary but per the Offer agreement and those the IRS can apply as it sees fit.

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