Hi Diane,
Your son will be able to remain in his stroller while waiting in line. There are a couple of things that you need to do to help facilitate this. When you are at Guest Relations getting the Guest Assistance Card for him, tell them that he uses a stroller instead of a wheelchair. They will need to stamp the GAC to indicate that "Guests can use their stroller as a wheelchair" in addition to the "Guests can use an alternate attraction entrance, where available". Also be sure you obtain a red band to put on his stroller. Make sure you put it in a location that Cast Members can easily see - I usually put it on the handle of my son's stroller.
If you do not have the stamps and band, you will be asked to park the stroller the designated stroller parking areas for an attraction.
There are some attractions where a Cast Member may ask you if he can transfer and if he is able to stand for a short time. If so they will ask you to leave the stroller near the exit of the attraction and escort you to the alternate entrance. The Haunted Mansion is one that comes to mind. Be sure you park it where they tell you - otherwise you could return to find that it has been moved to the regular stroller parking area.
Be sure to check out the Guests with
Mobility Disabilities section on the WDW website. I am also happy to answer any additional questions that you may have during your planning to make this a stress free and wonderful vacation for you and your son. Wishing you many magical memories :-) Allison