We have a B.O.B. Revolution Duallie. It's accompanied us on every trip for the last 5 years! We love Bob, and would be lost without him!
As long as you have it folded up before the bus pulls up, it's not a problem. My hubby handles the stroller though. I handle the bags and kids.
He just moves towards the back and keeps it leaned up against his legs if he's sitting or standing. The biggest thing for us to keep it from bothering other guests. We usually put the kids in the bus seats behind the area that the stroller blocks. They don't need the leg room anyway.
On the boats there is usually a spot to stow the stroller. It depends on how crowded it is though. Sometimes you just have to keep it as tight against you as possible to keep it out of the way.
Having the stroller is far more convenient than doing without it, and the Disney strollers are awful. They're hard, difficult to steer and only available in the parks.