Carried the plans in our bag when we went to each park - worked really well. Gave us something to do when we were in line - plan out next move!
We did stop whenever we wanted to sit, eat, shop, go on a ride that wasn't "in order" if there was a small wait. We even skipped some attractions altogether.
I think the guide is to help you make sure you get to see the most popular attractions in an efficient (map, walking) kind of way. Basically they put the attractions with fastpasses early in the day to make sure you get to see them and even get fastpasses to get back on.
It's a LOT of walking in each park, so if you see something you want to stop at and it's not too busy, I would recommend stopping, rather than trying to come back later.
Were there at xmas, very busy, so things like Soarin' ran out of fastpasses by late morning. I'm glad we followed the plan to do that sort of popular ride first.