The first thing is to make sure the diagnosis is accurate; if in doubt, see a dermatologist or other expert. I question it in part because warts are not very common on the scrotum; they occur there, but a lot less frequently than the penis.
To answer you specific question, different people tolerate the various therapies diffferently. None of them is perfect either in effectiveness or side effects. Condylox may work better for you, and may (or may not) be less toxic. In addition, there are several treatments that doctors can apply in their offices. If a dermatologist confirms the diagnosis, s/he may treat you with freezing, electrocautery, laser therapy, or even surgical removal.
Good luck-- HHH, MD
Just to clear things up, the warts are not on my scrotum, they are on the base of my penis. When I would apply the Aldara to the base, it would rest on my scrotum and the medicine would get on the scrotum and burn it. It has left pretty bad scarring there, the skin is basically white now. That is the least of my worries though. Thanks for the help.