S.S.
You want a biological enzyme cleaner - you can buy them at pet smart or any similar store. Pick one, follow the directions - make sure to soak up the pee as best you can with a towel, then soak it with enzyme stuff to an inch or so outside the pee area (pm me if you want to know why) - and let everything air dry (takes a day or so).
The cleaner works real well around the base of the toilet and stuff, if your boys have problems with aim.
If you still notice smell, get a black light (some cleaners come with one - which is totally worth the cost). Turn out all the lights and treat the things that glow. When you've got it done and it dries, it shouldn't glow in black light.
S.