You can wait at any stop you want to. The one closest to the tower will be Bus Stop 1, at the front of the resort. Stop 1 is the last pick up and last drop off for all buses, except for Disney Springs where its the first bus stop picked up and the first dropped off. The benefit to being the last pick up is that you'll head out to the parks as soon as you're board, so no circling the resort for the other stops. The con is that it's often standing room only at that point, especially in the morning.
Bus Stop 2, which is past El Centro near Casitas, is the first stop picked up and dropped off for the parks (except Disney Springs). If you're eating breakfast at one of the restaurants in El Centro, it would be an easy walk over to Bus Stop 2 from there if you wanted.
The bus times are only visible on the app when you are on-site. You'll be able to see them once you're at the resort.