You've opened a huge can of worms. A manual gives you a lot of control over the car, and there are a million answers depending on your conditions, driving style, and skill level
Sounds like you're figuring things out ok though. There's a lot of debate on engine braking under normal driving conditions, what with all the subtle tradeoffs involved in terms of maintenance and wear on various things. Personally, I tend to engine brake a lot and save myself some brake wear, I haven't ever experience any engine life issues from it.
Also, there's not much point downshift to 1st in most conditions. It can really wear on some components and isn't all that useful. Once you get low on revs in 2, it's probably best to just put it back in neutral and brake the rest of the way to your stop (or stay in 2 and/or coast in neutral if you're just going through a corner and then re-accelerating). If you were driving on a track and coming through a corner so tight that it demanded first gear for the exit, it might be a different story, but it doesn't sound like that's the case.