Assuming you are using BW version later than 7.0, when you go to edit the end routine, a popup dialog will display with two tables in them. The right hand side table should contain only the fields that are being populated using the second transformation. All the fields that you don't want overwritten should remain on the left hand side table.
If you are on 7.0 or before, hit Ctrl+Shift+F7 and choose the first radio button.
Good luck.