Matching transactions multipay

Hi

i am assuming that he has done this for not just one pay run but for multiple

I am also assuming that you are using bank feeds

so my suggestion is to hide the bank feed transaction and manually reconcile the two pay employee transactions, obviously ensuring that they do balance

If this is in fact how your client intends to continue you could educate them in the use of electronic payments, or if that is not an option then perhaps allocate the account the pays are paid from to a clearing account and then when they are paid from the main bank account the transaction would be allocated to the clearing account. This doesn't mess up your general ledger, the clearing account can be reconciled to make sure there is no discrepancy 

hope that helps

Lisa