Payroll tracks the liability being accrued (from employee withholding plus any employer portion) on a per tax basis as you post employee checks or employee adjustments. It also keeps track of which G/L account IDs are being posted in, in relation to the tax liability.
When you run the Remittance Checks command, the program shows the liability that has been accrued on a per tax basis in the top portion of the window. In the bottom portion of the window it also shows the current account balances for all the liability G/L accounts that have been posted in relation to the tax authorities listed. Then, when the remittance check is posted, the accumulated tax liability information is reduced by the amount remitted. This means that if you decrease the amounts originally shown, there will be left-over, unpaid tax liability and the G/L liability accounts are reduced by the amount displayed (or entered).
In the “simple” case where the G/L accounts configured for a tax are used only for that tax (in some cases using the same G/L account for closely related taxes makes sense) and the account is posted to only through payroll processing, then the amounts shown at the top will match the amounts shown at the bottom. If the check is posted without modification, both the tax liabilities and the G/L account balances will be cleared.
If the tax liability amounts (top portion) do not reflect the true liability, the two most likely causes are:
1. This is the first remittance check after converting data from BPI.
2. The default amounts have been overridden previously.
If the G/L account balances do not reflect the appropriate amounts, the two most likely causes are:
1. General journal entries have been done against the account.
2. The accounts have been set as configuration accounts for other purposes.
The amounts shown as default tax liabilities can be reset(edited). You do that in Payroll/Configure/Taxes. For any given tax, if you right-click on the Current liability field you can choose to override it.
If you find that the G/L accounts related to taxes need to be cleared of extraneous postings, then general journal entries would be a straightforward way to do that.