What I do is introduce the fish and make sure sure that it's eating before adding any medications. Unless you have a finicky species, this should only take a day or two at most. I've learned to make sure they're eating before adding medications because some medications negatively affect appetite and if this turns out to be the case, it's good to know that a quick water change should induce feeding again.
Once the fish is eating and not showing symptoms of anything else, I treat prophylactically with PraziPro for the first week. This is a stress-free and effective treatment for flukes. This is a good time to observe and try to identify any disease or infection, trouble acclimating to captive life, and training to eat various prepared foods.
If all is well after the first week, I do a large water change and do another round of PraziPro, which is recommended to rid the fish of any flukes that may have been eggs in the first stage. I also start 1/2 dose of Cupramine the following day. I've learned the hard way to treat for cryptocaryon and amyloodinium regardless of visible symptoms. There are possible long term effects to the fish when treating with copper, so this is something you'll have to decide on your own. 48 hours after the first dose of Cupramine, I administer the second 1/2 dose and hold for 3 weeks. After that I'm confident enough to add to the display tank.
This is my ideal regiment for a fish that doesn't show unexpected symptoms. Obviously problems arise and you may have to adapt.