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I think my payroll liabilities might be out of whack

I just took over for our book keeper.  We have a payroll bank account.  At month's end, it should zero out, unless I'm looking at this wrong.  I transfer gross amount of check into payroll account.  Then print out checks for employee for net amount.  The taxes/insurance remain in payroll account.  Once a month I go online and pay the taxes/insurance which deducts from this account.  I try to do this on the first, or even last day of month.  When I run "custom summary report" it shows a negative net gain for the exact amount that I paid for taxes and insurance.  Payroll deductions are set up as liabilities.  When I pay the taxes online, I then create an entry in the register for the paid amount.  Am I doing this right? The report just seems to mess up.  Thanks.