I think it will depend on the vet, however, I would expect to pay for each of the fecals. Two poops from different chameleons means two separate tests need to be done.
My vet will do fecals for $20 a pop, but will not prescribe meds on a cham he has not seen. My advice is to take one cham in for a full check up- if there is a parasite present you can follow up with the rest, otherwise, if it is husbandry changes, you have not paid for multiple visits.