VAT Suspense and VAT control account

Hi - My VAT suspense account is showing an accumilated negative balance. this should be 0.00 when reconciled isn't it? the reason been - when I record payment for VAT , it doesn't record it from the actual bank account the money has gone out from. so I need to record anothe payment out from the bank account it self to clear bank transactions. this creates duplicate entries on VAT suspense account. how do I solve this?