While treating for parasites is very important, treating the resultant ulcerated area is equally important. Some will say to use hydrogen peroxide, then iodine, then dental adhesive to cover the wound. I have no argument with using all three if they are available and you're proficient treating with all of them so the fish is not left on the table too long.
Most people are not. I've treated many many koi and the only topicals I've ever used are iodine, Gentian violet and potassium permanganate (in that order). All are extremely effective. I swab the wound thoroughly with iodine, making sure to get underneath the skin and/or scaled edges. Remove any loose scales during this treatment as they will fall off anyway. This is generally a one-time treatment. Further swabbing if any healing is evident will injure the new tissue which is slowly forming around the wound (pale pink to white in color). Further deterioration of the ulcered area after a thorough swabbing indicates the need for a more accurate parasite discovery or a more accurate dose of antibiotic or a change in the antibiotic used.
The alternative to iodine is Gentian violet. This seems to work equally well and since it initially colors the area and then fades as it wears off, is equally as valuable as iodine as an indicator of healing. Gentian violet is available as a non-prescription med at most Walgreen/CVS pharmacies.
A third method is a drop of water on a tiny number of potassium permanganate crystals is only suggested if everything else seems to have failed. This not only kills any bacteria in the area but has a detrimental effect on the flesh which it touches. It kills tissue in the area, so be careful how far you swab with this. I use it in extremely difficult cases where it becomes a kill or cure situation. I have had success with this and I have only used it after I've tried everything else. The area treated takes several weeks to recover where areas treated with iodine or gentian violet are only a few days.
Swabbing is generally done with Q-tips. I have used a super sharp sewing tweezers to apply PP under the scales where there were pus blisters evident. That worked very well and the fish (a Yamabuki Ogon) is fully recovered and swimming in a client's 10,550 gallon pond as of 10-17-07.