I would give the medication as directed. With parasites, it depends on the load; most animals can carry low loads with no ill effects, but there's no way to tell when or what may cause a low load to blossom into a high load and make the animal seriously ill. Generally, the higher the load, the more difficult to control or eradicate, and eradication is best.
Parasites are generally passed on through contact with contaminated feces, so it's important to disinfect everything that may have even traces of feces on it—floor, screen, glass, branches, soil, leaves... everything. This includes places he may not have ? on directly, but his cloaca may have dragged across. This may mean getting rid of everything in the enclosure, then disinfecting all surfaces—solid or mesh—and starting over. F10 is one common veterinary disinfectant, but ask your vet what to use.
I wish the news were better; I've been through this with several dogs infected with various worms & coccidia. Fortunately, my lizards have all been clean.
