Please go to my question "Atypical urine cytology, but negative cystoscopy?" You should see it above in the discussion thread. There, you will find an answer I received from Dr. Bandari. I, too, was concerned about the atypical cells found in my urine from a routine urine test.
Dr. Bandari explains that there are other conditions, such as inflamation or infection that can cause atypia to be seen in urine, and that atypia does not necessarily correlate to pre-malignant or malignant conditions.
It's been some time since you posted this question. How have you made out since then with your situation?
Hope this helps.