The posting to the bank account is set from the Payruns window tab > Settings. You could process all employees under one bank account and then under the Pay Checks windows tab redirect the appropriate checks to the correct bank account.
If you will be using NV2 to upload EFT Deposits to the bank, you will need to setup a separate bank account for EFT Information including the EFT Information for the employees. A separate EFT Payments journal should be used as well.
Regards to All,