First of all, congratulations to you on being proactive and doing your homework, learning as much as you can.
I've never heard that most cf babies culture e.coli, and that just doesn't makes much sense to me, but maybe someone else can shed some light on that for you. If not, please ask the clinic more questions about it.
Emily started cpt when she was 5 days old, the day after her diagnosis. If you are trained by a qualified respitory therapist, you will not break ribs or endanger your child in any way. Please push them to train you NOW!!! If you wait until she is a few months older she will FIGHT you everytime you have to do it. IF you start now while she is small, it just becomes something you do, and she won't know any different. Also, not doing it NOW and allowing mucus to build up sets her up for more respitory infections as you get into the colder months. There is NO reason to wait with cpt, and I think most people here will agree.
With your nebulizer you will probably get albuterol (or, she might take this in a "puffer" inhaler form like for asthma...) and probably Pulmozyme. Maybe Flovent (also a puffer). These (in order) hlep to open the airways, break down mucus and reduce inflamation of the lungs. Basically they keep her lungs clear and healthy. We started with Albuterol immediatly, and then added the nebulizer when she first cultured psuedomonas at about 6 weeks old. We have done some combination of the above things and inhaled antibiotics ever since.
Prepare yourself to really push the doctors and nurses to get the best for Alexa. I would ask that they start you on pt now and do the inhalers/nebs that go with it NOW. Her health is too precious to waste!