don't feel bad or like a nuisance for contacting your CF center -- that is their job and they are there to help you! at my adult center we contact our doctors directly, not through the nurse, and when i started getting sick more often i felt terrible b/c i thought i was taking up too much of my doctor's time, etc...she finally figured out that i felt that way b/c i would apologize at the end of each email, and she basically told me never to feel guilty about helping her to do her job by keeping her in the loop as to all of my symptoms. it's a lot easier for them to treat things as they come up then for them to have deal with an emergency later. not to mention a LOT better for you son, as i'm sure you know.
that said, if i had a clinic visit scheduled for the next week and had a minor digestive issue, for example, i would probably just hold off and talk to them about it at my visit. but i also realize that i'm adult who has been living with my particular brand of CF for 28 years, so i have a pretty good idea of what can wait and what requires more immediate attention. if i were a mom to a young CF child i would probably be a little more aggressive about the more "minor" issues. and for what it's worth, my parents were just like you when i was growing up...they always kept the CF center totally informed and contacted them with every little problem, and i firmly believe that's why i was able to do things like move across the country for college and law school. persistence often pays off with a disease like CF.