Hm, you are updating the same columns in both cases. The order is different, but that does not matter.
But say that you want to update col1 when effectiveDate is NULL and update col2 is it is non-NULL. This is how you can do it:
UPDATE tbl
SET col1 = CASE WHEN effectiveDate IS NULL THEN <some new value> ELSE col1 END,
col2 = CASE WHEN effectiveDate IS NULL THEN col2 ELSE <some new value> END
WHERE ...