If you're getting the "stop letter" from a posted timetable, you should find a map showing where the stop is somewhere nearby. I'm sure you've worked out that popular locations in London (e.g. rail stations) have far too many bus routes running past them for one stop per location to be able to cope, from memory Waterloo station has about 20 different stops and if you find queue at the wrong one you'll never get the right bus!
Bus numbers work the same as they do anywhere else and aren't related to stop designations so don't be misled by that! Some bus routes have letters rather than route numbers, where the 999 route numbers available weren't enough for the number of routes, but again the route designation doesn't relate to the stop identification so don't expect that to make sense! Also on some routes there will be a route number, and the same route number with an "N" - e.g. 56N - that's a night bus and follows a slightly different route to the 56, but will serve the same major places.
If all else fails, find someone who looks like a commuter and ask them...we spend hours staring at tube maps and bus routes on our morning and evening trips, I know some who've learned by heart the various maps and routes as a way of passing the time on their journeys and would be delighted to be asked!
If I can be any more help, let me know, I spent six years commuting by London bus before I escaped to the countryside so I know a fair bit about the Capital's transport systems!
If you look at the little signs on top of the bus stops, as well as the route numbers and stop ID letters, they normally say "Busses towards London Zoo and Madam Tussauds", for example, or things like that, so there's another check.