Your cash account? That had to decrease because of this expense.

Hello, thank you for your reply! 

The problem is that I can't find where on Turbotax Business (form 1065 partnership tax return) to enter these late sales tax payments, and so on Turbotax, my balance sheet does not reconcile. 

In real life, my LLC's bank account has $29 in it. But in Turbotax, it looks like it should have ~$6500 because I have not found where to enter the late taxes and fees I paid.  

Understood but the money had to come from somewhere and there's no place to enter the payments because they don't belong on the return....they're pass throughs as sales tax that are collected from customers and paid to the taxing authority. Your balance sheet can reflect the payments but the $$ to pay the taxes came from an asset account or was borrowed.