I think I suggested Footprint as a guidebook. They generally have an overview of how to get in and out.

There is a general schedule of bus routes for Ecuador at www.ecuadorschedules.com

In Peru I tried to use Cruz del Sur for long distance travel, or tourist services such as 4-M or Inka Express. For the north in Peru I used Linea or Movil. Most front desks can advise you of the best/safest bus companies in a region (they definitely are not the same).

In Bolivia I flew when it was an option, there are tourist services between cities as well. Another vote for Kanoo Tours in La Paz, if you need local advice.

Re not being fluent, you can always pop in to a tourist agency or upmarket hotel (as well as backpacker hostels) and someone will be able to help translate.

Intercity buses in Peru are good and luxurious. One I rode years ago even had a stewardess who organized games and singing and handed out lunches. You haven't had a good time until you've taken a long bus ride with Latinos, particularly if you speak Spanish.

One exception to taking the bus everywhere is Cusco. I would think about flying there from Lima as a flight takes an hour but a bus takes around 22. OTOH, if you take the bus, it may help you avoid altitude sickness as you have time to get used to the changes in altitude.