Hi Lisa, thanks for posting on the Community
Once the payment has been manually made, this will be downloaded to the linked bank account the same as any other transaction.
Depending on the details entered when making the manual payment, it may be visible as to which payment is for which employee.
If you don't want staff to be able to access this in QuickBooks, you can change their user-permissions to a standard user with limited access to customers and/or suppliers. This way, they'll still be able to perform specific roles, but won't have access to the banking feature.
To view the full user roles and access rights, click here. Get back to us if you have any further Q's. :)