Well.... my soul 'absorbs inspiration' from a variety of areas and experiences, before filtering out the ones which seem the awesomest, then I use those as a base for my protagonists. I solidify their en general, general appearances and personalities por giving them my own traits and qualities, so that I can connect with them better and basically express myself through them. However, I give them certain things which sets them apart from me uniquely.
To sum it up, the protagonists are different versions of my own self, just with some qualities which I'd like to have - but currently don't (e.g I'll give them blue eyes, because my eyes are brown and I think they're boring.... o I'll give them magical powers, which I obviously don't have!).
The protagonists' enemies, friends, those other people.... they're then conjured up por my mind, mostly based on my own enemies, my own loved ones, etc.
I don't really come up with them: they come to me.
Usually, if tu have a story idea, your main characters just come with them. They typically balance each other out automatically. If tu need a minor character though, think about the role tu need that character to play in the story and go from there. Decide their personality, and base their appearance off of that. If tu can't think of a role though, tu probably don't really need that character.
I come up with the plot first and then I come up with the characters cause whatever my plot is that's how I decide what I want my characters to be and what they'll do and bring to the story. I hope that makes sense :)