With regard to employee expense payments, you can allow ACH payments to the employees by defining the ACH payment under Financial Settings on the Employee record in Configuration.  This is not an area you want the employee to access on their own, and not something you want to open to the AP department to keep updated.  It would be nice if the employee could choose their expense reimbursement method (if allowed), check or ACH, and allow them to maintain their own bank information for ACH payments.  That way they can also be responsible for upkeep if they change a bank account, etc.  This is obviously something that would need to be secure.