First, let me say that I am sorry to hear of your son's illness. Pulmonary Alveolar Proeinosis is a complex disorder that may result from genetic or other causes and is quite rare. I'm sure that there are many important questions for you to ask his doctors and one important thing is to remember that you don't have to ask or learn everything at once - becoming familiar with this will necessarily be a process, not an event. You might want to start with making sure that you understand how his diagnosis was made, what if any additional tests are necessary to confirm the diagnosis and what sort of care he needs now. Care he needs now would include medications but also nutrition (which is often very important for infants with chronic disease) and can impact lung function. Given the rarity of the diagnosis, it is fair to ask his doctors how much experience they have in managing infants like your son. If they don't have much experience it is also very reasonable to seek another opinion at a lung transplant center - even if he doesn't need a transplant now, a transplant center will likely have more experience in managing the disease. Finally, you might want to ask if the team can provide you with contact information for other families who have faced this disease and can share their experiences with you. Once you are more settled with the diagnosis and current care you can think more clearly about options for the future.
Again, I am sorry that your son is ill and I hope you will find this answer helpful. Please reply if you have any follow up questions.