As far as learning to dial in an amp, I've never had two that dialed in exactly the same way. Every time I've gotten a new amp, I've had to learn how to dial it in to get what I wanted out of it. So, don't worry too much about what you learn on one amp carrying over to other amps. There are simliarities in operating all amps, tube and/or solid state, but the specifics change.
What I'd advise is find an amp that you like the sound of generally, and learn how to work it. Read the manual and any other info you can get on it. Talk to other people who have the same amp and see what they do with it. To paraphrase Ray Charles, learn how to make it do what it do.
Pedals are not often a problem, not with any amp I've ever used. Frankly, amps of every sort are designed to work with pedals, or vice versa. And, there are so many different sorts of every kind of pedal that's ever been invented that if you don't like what one does with your amp, try another one. I'd just about guarantee you'll eventually find ones you like.
Finding out what you like by trial and error is all part of the fun of playing. Read the available info to learn what the rules are, because you need to know them in order to figure out how to break them. That's when it get's really fun...
SEND FORTH THE BERSERKERS!