If you start writing a manuscript, there is a fairly good chance that you already have your protagonist in mind, maybe even several of them. If not, this really isn't a big deal, it just means that you have the start of a plot-driven narrative, and the character is only slightly less important than your story (caveat) so far.
The who, what, and where of your protagonist is more important than their physical characteristics. Take this into mind: Each reader is going to identify with your characters differently, and there is a very strong chance that they are going to picture them differently in their mind than you do. Their interpretation of your character is based on a 50/50% mix of your physical description and a host of other factors that are entirely out of your control. With this in mind, sketch out a rough idea of who you want your character to be, with a general idea of how they look (usually as it pertains to the role they fill, or their stature as it relates to other characters around them). Think of balance. If you overemphasize how they look, scrutinizing them down to every freckle, wrinkle, eye lash, and bulging muscle, but fail to flesh out exactly who they are underneath, your readers are going to be left with a very shallow, and unrelatable character that they can picture very vividly in their mind, but have no emotional connection to. So instead, try and articulate how your character talks, and what makes them tick. This is important, and will help you develop them during dialogue and important dramatic moments. What about their history has made them the way that they are? Just as in your concept, back story is a wonderful, and sometimes underutilized tool. Are they mysterious, or just misunderstood? Do they have a scar? What fated meeting in their past left them with such a blemish? As you start out, it is not a bad Idea to focus more on who you want your character to be, than what they look like to your reader. Another important thing to remember about your characters is this: Each and every one of them is representative of something, and it is up to you to identify what that is. Writing is a very personal, and emotional experience for a writer. You will feel connected to your characters (yes even the bad ones). You will know what drives them, angers them, and makes them happy. At one point, they will feel like they have become a part of you, and if you achieve that, you know that you have succeeded. With that said, put a little of yourself into each of your characters. The stuff you like, the stuff you don't, and the stuff that you wish you saw more often in others. Look at the people around you, those people that love and nurture you, support and challenge you. What is it about those people that intrigues you, but moreover, what about them could you translate into quality protagonists/antagonists, or supporting characters. It is important to craft your characters so they are believable, so don't give them skills, powers, or abilities that seem unnatural or excessive (Yeah, Swiss Army Knives are cool, but remember, they're just pocket knives). People who read books are looking for characters that they share some common thread with, relationship problems, money, an ailment, or a speech impediment are a few examples, so it is important that you keep them human, and in many cases, humble. I recently read a book where the main character was completely unrelatable. They were cocky, brash, and completely unpredictable in a world where they could ill afford to be. These were all faults with the character that affected the story, and the characters around them more than the antagonist(s) did, and from my perspective, was quite frustrating. I found it incredibly hard to like this character, and what was worse, as the story continued, they did nothing to change my impression. I put down the book and instantly disregarded the rest of the series, based entirely off of the fact that I could not connect to the protagonist, and worse, that I had zero investment in their continued survival, or exploits. I do not say that lightly, as the author had an intriguing concept, and was a very talented, and polished author. So, in a nutshell, that is why it is crucial that you put ample time and consideration into your character(s). You want your reader to draw that character in, to develop an emotional connection. You want your reader concerned for your character's well-being, not write them off. Next up, in Part Three-Constructing your Narrative, I will talk about the body of your story.