It is possible that your GP wants to find the exact cause of your symptoms and where those symptoms originate. Generalised abdominal symptoms can (though not always) be caused by a problem with the bowel, having a procedure to look at bowel health would be common sense. Occasionally symptoms are ambiguous when it comes to the kidneys and my guess (I must stress here that I am no Doctor) is that that if your bowel proves to be healthy then more tests will be carried out to see if if your problem relates to your kidneys or elsewhere in your urinary tract.
I am sorry I can't help with anything related to the procedure, I have had the camera down the throat test twice and though uncomfortable it was not painful. Good luck.