Need Questions for Doctor

Following surgery to remove a cyst in late Nov., the desease wasn't discovered until after a biopsy on the cyst.  Chemo was started in Dec.  My wife had one chemo and then a CT scan.  We know that this is not the "normal" procedure, but based on the CT scan, she moved from Stage 1 to Stage 3C.  After the 4th chemo, she had surgery.  The chemo had reduced the 2+ cm tumors to not visible to the eye.  The surgeon removed her omentum.  The biopsy show that there was a lot of desease present.  Based on that, the surgeon said that there must be cancer in the areas where the tumors had been present.  (This made sense to us.) He recommended a total of 8 or 9 chemos rather than the usual 6.  Our oncologist disagreed.  Based on research and how my wife is doing, he has referred her to a radiation oncologist.  Most of what I have been able to read is dated 1996 to the present.  I don't understand how the radiation oncologist will know where to focus the radiation if the tumors are not visiable to the eye or in a CT scan.  I have read that PET scans can suggest that the desease is present.  Have techniques changed so that treatment can be given to the whole abdomen without damaging other organs?  What questions should we be asking other than those that I have asked here?

Thanks-
Paul