There are actually 3 columns...Payments, Deposit and Amount and then the Balance column. Amount can be for either deposit or payment. Depending on the sign + or - in the Amount column it will also put the $ in the appropriate Payment or Deposit column.
That extra Amount column can be confusing. I would delete it and just enter the $ in the right column, either Payments or Deposit. Click on the Gear Icon right above the balance column and unselect the "Amount" Column (1st one) and make sure the Deposit and Payment columns are checked. Payments is at the very bottom of the list.