One solution is to allow both methods.
You can make a data entry field called [EE number direct entry].
Then you already probably have [Related Employee number or whatever the current relationship reference field is called.
Then have a formula called [Employee # (final)] field like
IF([EE number direct entry]>0. ,[EE number direct entry], related employee number])
Then make a 2nd relationship to the Employees table and get any lookup fields only from that 2nd relationship.