Create relationship with duplicate values

Table 1, Table 2 and Table 3. Table 1 Col A values are there in Table 2 Col D & Table 1 Col B values are there in Table 3 Col F. While creating relationship from Table 1 Col A to Table 2 Col D it through an error as " You cant create relationship b/w these two columns because one of the columns must have unique values."

These are Emp id 's ..40056 is the emp id of Mr. John at x location and 5727812 is the emp id of Mr. John at y location.

If there is a case like 

Mr. Peter is there only y location he doesn't have any presence in x location.

I need to figure out respective timesheet hours for each location. Because of duplicate values (spaces in Col A) we are not able to create relationships. Is there any way to create a relationship without disturbing null values in Col A.