We have a very large amount of cusomter cross-reference part numbers to enter.  Is there a way to import an excel file with this information into the system rather than enter then one at a time?

Actually, the customer cross reference is not one of the fields that can be imported using the standard Import Inventory program.  You would need to use ODBC and Access or some other program to import the data.  The file you need to populate is BKICREF.