Everyone does things differently. That's a good thing. Watch, read, learn, adapt for yourself. Don't get caught up in what's the right way to do things because there is no right way. There's what looks good and what doesn't. In the end, if it doesn't look good then you need to try something else.
With that in mind, here's me in a nutshell.
I learned how to shoot by reading books and message boards like this one. I learned how to make a narrative movie by doing it (check that, 'still' learning). The more I do, the better I get. I think that goes for everyone. Don't sit around and read how to do it. Go do it. Or better yet, read one "decent" book about doing it, then go do it, then come back and ask questions about doing it, then go do it again, only better and maybe pick up on some more reading.
I write the scripts I shoot so maybe some of this won't apply to you. Generally, a movie my team and I do goes like this.
1. I write the script and we have a meeting where everyone reads it and critiques it. I change what I feel needs changing.
2. I sit down and draw storyboards of how I want the film to look, shot by shot. These are detailed and include scene breakdowns, what shot I want to use, cuts on action, notes about sub-text, things like that, so when I get on location it's easy to remember what I was thinking when I wasn't limited by time, light, and space.
3. We scout locations. I have a pretty good idea of what I need and I'm very familiar with my area so I can usually find what I want.
4. We show up on location and shoot. When I do my storyboards and scene breakdowns I also run through and figure out the best order to shoot. Things change when you're on location so I keep my storyboards in pencil and not chiseled in stone. Be free to change the script and the look but don't stray too far away or your movie won't have that consistent feel to it.
4.a. Once I have the order of shooting and the place we're going to shoot, the actors get together and rehearse. Having inexperienced actors myself, I anticipate they need some help with how, where and when to move or stay still. Once the blocking is worked out and we set up and shoot the wide stuff first (remember this bit for later). Then get closer as the takes stack up and the actors are beginning to hit their stride and know their lines and have gotten into their roles more. Some actors take longer than others and you have to watch closely that one actor who's 'mojo is werkin' doesn't shut down because the other actor needs 15+ takes.
4.b. If I see the actors flowing nicely and now they are sure they have their lines memorized, I'll re-do the wide stuff because their movements are more natural. Sneaky, perhaps, but I have learned that having the cameras rolling adds pressure and this pressure helps focus untrained actors. Tape is cheap, use it up. So actually I end up shooting the wide stuff last and the beginning is just a taped rehearsal. I find the actors learn get into their stride faster when the pressure is on, or the tape is rolling, or it's live, how ever you want to say it.
4.c. Getting coverage means getting more shots than you want or think you need so you can have maximum freedom when you edit. Personally, I don't do much coverage (yes tape is cheap) and the storyboard is just a guide to help me hit the right beats of a scene but I've learned to trust my instincts and go with it. I really like keeping an open mind about what shots to do when I'm actually on the location but the shots I pick, I trust.
5. Speaking of coverage, every scene needs some ECU isolation shots. If I was shooting a movie with an escaped caveman, I would get ten seconds of his fingers fondling the chain or something like that because when you edit, things like that save your continuity butt and your editor will love you. Or if you're like me, you'll love yourself. A hand going for an ashtray, a cube of sugar soaking up some tea, something that helps the narrative or the mood of a scene can really save you in the editing room so I do this a lot.
6. Cast and crew will get bored. Sometimes they'll get frustrated, maybe even angry. All you can do is stay relaxed, keep it light, and make sure you have plenty to drink for everyone.
Which shot to choose. Good question. Watch movies and learn. Det. Harry Callahan played by Clint Eastwood, in Dirty Harry, written by Joseph Stinson says "Go ahead, make my day." Notice the camera is slightly below his eye line showing dominance. The assailant is standing up with a woman in his clutches and a gun in his hand.
But in another "Dirty Harry" film the assailant this time is laying the floor, his hand is almost touching a shotgun. This time the camera is way lower than the eye line showing not the assailants point of view as much as one of the cafe's customers who's really close to the action. This way you're pulled close to the action as a bystander and you're not being asked to sympathize with the assailant because the very next shot of the him giving up is slightly above his eye line. Just as a crouching victim would see it.
Which shot to use depends on you the director and your style and the narrative of the story you want to tell (which may or may not agree with the author of the script).
Who do you want the audience to relate to? Who should the viewers sympathize with in any given scene. What feeling do you want to invoke, getting your actors to emote this is only part of the battle. You need to show it through which shot you choose and how you choose to show it. Lighting, sound, environment, all these things combine to make for a beautifully shot movie.
Where do you go the learn them? Film school is a choice I think you need to make after you've heard both sides of that argument and it is a very heated argument so be prepared. It's also something I don't want to get into here. Instead, let me recommend these books:
"Film Directing Shot by Shot" by Steven D. Katz,
"Film Directing Cinematic Motion: A Workshop for Staging Scenes" (Film Directing) also by Steven D. Katz,
"Directing Actors: Creating Memorable Performances for Film and Television" by Judith Weston,
"The Film Director's Intuition: Script Analysis and Rehearsal Techniques" also by Judith Weston,
"Directing: Film Techniques and Aesthetics" by Michael Rabiger (I haven't read Rabiger but I plan to because I've heard so many good things about it).
Like I said above, 'read' and 'do' at the same time is the best advice I can give.
Hope this helps.