So.... as stated elsewhere, I'm new at the craft of storytelling.  I've been writing for decades. But I am trying to make a serious go at doing what I have really always wanted to do: write and get published.

I've got this story I've been carting around for two years, that I have taken periodic whacks at; but  have run up against my perenial problem: I'm flying by the seat of my pants and I'm not really very good at it. So I'm taking time to learn the craft, how I can approach it differently and prevent myself running out of steam.

I am sticking with this story because its the first time in a very long time that I have had a beginning, middle and end. And I  like it.

So I'm working on the plot and the characters, and I realized last night that my protagonist is not my protagonist.  He's an important player, in fact he's the goal that both the actual protagonist and antagonist have set their sights on. It is an m/m parnormal romance... and well, the guy I thought was my protagonist is actually the beta male. I was trying to shoe horn the characters into their roles, when they were obviously the opposite.

Ever happened to you? How did you realign your thoughts after realizing this or something like it?

I don't need to throw away anything, luckily; but it really does force me to realign my thinking.

 Stories do that, they take on a life of their own. Flow with it. I've added something before that is just the tiniest little itty bitty thing, only one line of something that might be interesting, and it decides to become the most important thing in the story. And I've had characters that were supposed to be important but ended up with no purpose. I usually just open the airlock and let them float off into space... bye bye failed charactrer. Or if you end up with a bunch of characters you don't need anymore you can just have a 'Red Wedding'. But then you get that one character that just refuses to die, that's the hard one, yea, then you try to blow up their planet to get rid of them, but they always seem to escape.

Yeah, that happens constantly, especially if a story is strong enough to be considered "alive" in that metaphorical way.  The thing with the protagonist: he/she doesn't have to be the central character, but he/she does have to be the character whose viewpoint the story is told from.  That's really all that makes the protagonist.  I guess you could say it's just a matter of page-time.  Protagonists don't have to be the "central" character; I've read some stories in which the protagonist was simply the observer.  I've read others in which the protagonists are passive characters and the other characters get to have all the fun.  I've certainly written stories in which the protagonists were passive, and the only thing they offered was a way for the reader to enter the world of story and care about the events and characters depicted.  If your story does that, it doesn't really matter who the protagonist is (on one level).  The thing to consider is how the story is written: even if your protagonist is not  the main player, the Top Dog or whatever, he or she should be the one that provides the context of the story.  If written in first person ("I") then it's a lot easier for the protagonist to be someone other than the alpha-male or whatever.  From 3rd person ("he" or "she") it's just as easy, but the viewpoint should probably be 3rd Person Limited, which just means that as the writer of the story, you limit insights, perception, actions, etc. to that character, and so the reader wouldn't know any more than the protagonist knows.  And that's the funny thing about protagonists, they aren't always the central characters, but they are the central viewpoint characters.  A perfect example would be Moby Dick.  Captain Ahab was the guy that got all of the action, but Ishmael was the guy telling the story, thus Ishmael was the viewpoint character, but Capt'n Ahab was the protagonist.  In a later novel, The Scar, by China Mieville, the central character, Bellis Coldwine, was immensely passive; she went along with the main-stage players, existing as the conduit through which the readers were able to enter the world of the novel, but everybody else got the juicy, dramatic bits, and she existed simply as either an observer, or the person who actually survived the whole thing simply because she wasn't constantly risking her life.  Now, in my own writing, I sometimes consciously avoid letting my protagonists and central characters be the same person, but all in all, it depends on what you want your story to be.  If your protagonist differs from your viewpoint character, this opens up emotional possibilities that simply don't exist if the viewpoint character and protagonist are the same person.

Makes you wonder what happens when almost every character is a protagonist or antagonist with almost equal importance. I speak as I begin to realise that those I thought were the most important are suddenly 'also rans', where every character has their part to play and all will fight to achieve the same goal as the climax to the story approaches. I have killed characters in the past, but it still comes as a surprise when I realise that this or that person has to die to move the plot forward.

Yeah, that's where writing gets fun (on another level) because each and every character you write is a potential main protagonist or main antagonist.  Just because they're in one story doesn't mean they're not going to come out and tap you on the shoulder and say, metaphorically, of course: "Hey you!  Write my story now."  If you have 5 characters in a story, that's 5 stories you can potentially write.  I love it when things like that happen.

 When your characters ask you to realign your thinking ... that's what you do!  Regardless of how much time it takes, or what a pain in the patootie it might be.  The most important thing is to be true to your story and make your characters as good as they can be.  Character development is everything, imho.  Take the time to get to know them yourself, and take the time to put all those details in.  And as has already been said, your alpha character doesn't have to be the narrator. 

Good luck, and have fun!  :)