Initially, there was a loading dose twice a day (for the first two weeks, I think), then the dosing went down to once a day. That was later able to be cut to half a tablet, once a day. We worked with the vet to get to the lowest dose that would be effective, because it's an immunosuppressant. Over two years or so the dog has had one UTI, possibly related to the Apoquel, but other than that no noticeable side effects.
As to the source of the allergies, you can get the dog tested. That may help you avoid certain specific foods, rather than just going by trial and error. We eventually settled on one variety of Taste of the Wild food, with occasional treats of chicken, and Cinnabone dog biscuits, and a marrow bone once a week or so. That was the result of a combination of the allergy testing, and trying things out.
As in your situation, we adopted our dog (she's a Border Collie) as an adult. The itching was pretty bad initially, but it's considerably better now.