Yes, assume the CYA you added is there and adjust the FC accordingly.
The CYA test is the mist subjective by far. The lighting can affect results tremendously. Experiment a little and see for yourself the next time you test it. Get a few readings with your sample out next to the pool in bright sunlight. Then go inside and take a few under bright lights, or flourescent lights. Also expeiment with holding the view tube with just one finger and thumb versus holding it with all your fingertips and your thumb. Take readings with the tube down at waist level and again closer to your face. Look away for a minute in case you get that afterimage optical illusion effect and then look at the tube again.
You'll have readings all over the place. If it really troubles you, when you need to order refills, order the CYA standard solution. It's a 50 ppm sample you mix and test to ensure you get 50 when you take a reading. You practice your technique until you find the combination that gives you the right answer. Then you just emulate those conditions when you test the pool. Here's a recent thread about it:
http://www.troublefreepool.com/threads/75708-CYA-testing
