Two here too. My teenage boys are four years apart. This is going to sound weird too, but I can't imagine what it would be like to have one without CF. My boys do the same treatments, meds, clinics, hospitalizations etc. In our house, its the "norm". Even my boys have said they are glad they both have the same issues.
If your question is how do you cope with the organization, we write down EVERYTHING. My notebook is color-coded for each boy. It does get complicated to be sure especially with scheduling if one has to go in.
If your question is how do you cope with the sadness, guilt, worry, I have no easy answer for that. Take everything one day at a time, love your kids to pieces and treat them like normal kids.
Do the best you can, some days are easier than others.