Electronic Payments issue in Bank Recconcilliation

Hi Millers_BA 

If I have understood you correctly you have two company files with a bank account in each. Within Company File 1, you have processed the pays for the employee but in the upload process to the bank, the funds have come from Company File's 2 bank account?

If I am on the correct track, it would be a matter of setting up a new bank account in each company file. For example, if Company File 1 you would generate a new holding account -- Accounts>>Accounts List>>New and give the account a number, name and set the account type to be Bank. You'll then need to enter dummy banking information into the Details section of that account. Once that account has been created, you would process the Electronic Payment to the account within that file.

In the other company file it would be a similar process of going to create another holding account  Accounts>>Accounts List>>New and give the account a number, name and set the account type to be Bank. Once that has been included, it would be a case of recording a Spend Money transaction from the required bank account to the holding account for that amount.

Note: The above processes will leave you with a balance in the holding account for each company file which could be included in a journal or another transaction to clear that account balance in the file.