I have a table structure something like this
table Employees
EmployeeID
EmployeeLogin
EmployeeCustID
table Customers
CustomerID
CustomerName
Is EmployeeCustID unique? If not, this is never going to work, as you then try to cram two different entity types into 1. Also, with your structure, how do you want to save an instance? -> the CustomerID isn't known, so you can't save such an entity.
IMHO it's better to simply keep Customer as a related entity to Employee, as (I assume) the EmployeeCustID is used to link a Customer entity to an Employee entity if the employee is also a customer, which means 'customer' is just a role for employee and therefore optional and changeable and thus should be a separate entity.