Hopefully you can get this resolved quickly enough that the following advice isn't needed:
Anytime you have a dispute with the IRS, send in the amount that they ask. NONE of the paperwork makes it clear that you can do this while still contesting the charges.
- I sent in the full payment to the address requested, I included a note that I was prepaying the amounts and had mailed in a dispute.
- I sent a dispute to the dispute address and noted that I had prepaid the amounts pending our resolution.
- The IRS send me a letter agreeing to my dispute which I had to sign and return. (Yes even though they agreed to everything I disputed, I still had to sign a document that I was in agreement with the new resolution.) IRS sent a refund check for the amount that was due to me.
Some people thing "With-holding a payment" can sometimes be used at leverage. However in my opinion the opposite is true with the IRS. Once you've submitted payment and have stopped fees from accruing they become very focused on getting the case closed.
- In my case, I never met, or spoke to an IRS agent through the whole process. I filed the dispute, they agreed, case closed.