My son has had this procedure done several times. During my first ultrasound, we found out that one of his kidneys was enlarged. So, when he was 4 months old, we took him to Children's for some tests and found out that he had reflux (he also had ureteropelvic junction obstruction, but that is another story). They did the VCUG at 4 months, 1 year, 3 years, and 5 years, with the condition lessening each time. At 5, he did not show any more signs and will not need any more tests! He was on a small dose of antibiotics to prevent UTI, which he took every day until he was 5. He is now 6, perfectly healthy, and not on any meds.
So, about the procedure itself... it was not pleasant to watch because they had to strap him down when he was a baby. At age 3, he did not understand what was going on, so he pretty much let them do it, although he cried or whined the whole time. At age 5, he refused to cooperate (even though the technician was very patient and willing to try anything, even a DVD) and we had to go back and do it under sedation (they gave him a drink which calmed him down and everything went well). They explained to me that the procedure is not painful, just uncomfortable. One thing I found out the last time we went is that you could ask in advance to have a person come who is specialized in entertaining/calming kids down for unpleasant situations - I forget the title they gave that person.
In situations like this, I just tell myself that it will be a few minutes of unpleasantness and then it's over... you can get through it! Good luck.