The best way to write a protagonist that isn't overshadowed by other characters is to write him the same way you would the other characters. There is nothing keeping you from writing a protagonist with just as many quirks and complexities as any supporting character. In fact, in the beginning, it may be best to avoid using terms such as "protagonist" or "hero", or even "supporting characters" and "villain". They're all characters and should be treated about equally. Don't let their role in the story define them. And if you find yourself in a situation where your comic relief is more entertaining than your main character, maybe you should think about switching perspectives.
I think there's a tendency for writers to want to keep their protagonists a blank slate so that everyone can relate to him and project their own personalities onto them. Or to keep their protagonists away from any vices and flaws so that nobody gets offended. Or else they intend on creating their protagonist to be the image of the ideal man, perfect in every way, because they some how believe that's the kind of hero people want to see.
Personally, I think the best heroes are the ones with a selfish streak. Yes, it's important that they have a good heart and do good things and such. But they should have at least one selfish desire, a goal that drives them beyond "I'm a good person, thus I should do good things". I think people can relate to characters more if they are a tad selfish. For example, I've created protagonists whose motivations for doing what they do include seeking fame, popularity, a girl, or a sense of self worth. Other motivations I think work for a hero would be riches, revenge, solitude, healing, and perfection. These motivations don't necessarily have to conflict with their need to do good things, and in fact, can be the driving force that causes them to do good things. For example, my character who seeks fame, does so by saving lives and being the greatest hero he could be. But things can be more interesting if these selfish motivations cause some internal conflicts. For example, should my protagonist who seeks fame meets a girl whom he likes very much. At some point, he'd be forced to make a choice between saving the girl he loves, or obtaining the fame he's long been after.
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Okay, here's Rinzen and the world. (As it's basically a Fantasy Counterpart Culture to the entirety of East Asia, I'll put in hotlinks to whatever a thing is equivalent to.)
I have decided that A: Rinzen's parents will be Zhangshani and Sheysacan, and B: they will not be important to the story at all. In-story, he first appears in the trading city of Golden Larch, close to the border between Zhangshan and Sheysaca, running away from something. He will be around age nine at this point. He is found by a Cultivator monk and taken to a monastery, where it is discovered that he has escaped from a group of bandits that were keeping him as a slave.
Rinzen went back to Golden Larch because he remembers he was born there, and was kidnapped at an early age on a raid on the town by woodland bandits. The implication is that this was done in order to bring in new bandits – he was to go on his first raid soon when he escaped. Before that raid, he was branded with a tattoo on his neck of the character “虫”, meaning ‘worm’. (In reality, those that ‘go on raids’ were actually tested to see if they could join the Brotherhood of the Golden Silkworm, an evil organisation. If they pass the test, the character is turned to the character for ‘poison’, ‘蠱’, and they gain Touch of Death skills. If it is not turned into the character for poison, the tattoo will sap their life, slowly killing them.)
He escapes the monastery, fearful that they will force him to be a monk, and ends up landing in a tomb. He starts to scramble to take stuff from the tomb so he can sell it and get food, then is angrily rebuked by the ghost of the tomb's owner. The ghost and Rinzen argue until the Cultivator monk who found him shows up. He and the ghost, whose name is Hin Xin, know each other already. Rinzen opposes further attempts to bring him back to the monastery, while Hin Xin complains at the state of his tomb, and says that nobody performed the funeral rituals for him when he died, so he's stuck on earth. (There is a very strong idea in Chinese culture that if you don't venerate your ancestors, they might not reach the afterlife and come back as ghosts on earth.)
Eventually, it is decided that Rinzen will work at the Cultivator temple, although not as a monk, and he will care for Hin Xin's tomb in the hopes that the ghost will be at peace and enter the afterlife. Rinzen adjusts fairly quickly to monastery life, although not so fast to aiding Hin Xin. Eventually they warm up to each other, and Hin Xin, who was a scholar-bureaucrat for Zhangshan in life, teaches Rinzen how to write characters. He trains him for the imperial examinations, the only way to get anywhere socially in Zhangshan.
Time Skip. Rinzen is now about to turn twenty, the traditional age of manhood in Zhangshan (and China, too). Hin Xin gives him the name "Snow Lion" (Chinese men traditionally got new names at age 20, although in Jiangshan this practice has mostly died out). (Rinzen has a serious Lion motif because White Lions are very important to Tibet and lions are fairly important to China.) By now, Hin Xin is less cranky and more welcoming of different ideas, and Rinzen is much less rough around the edges. The unfortunate effect of such character development is that Hin Xin is no longer bound to the Earth and so goes to heaven, leaving Rinzen by himself.
Rinzen is a Nature Hero, liking to Skyleap through the mountains near Golden Larch. He is sort of a Big Brother Mentor to most of the children in Golden Larch, although the adults don’t like him. His social skills are poor at first and then improve, but he is still not entirely at home in civilisation. This is where my problem is: I have a good backstory for him, but Rinzen himself eludes me. His personality is too vague, and I have trouble writing him much beyond my generic "snarky literate person" thing.

I'm trying to develop my protagonist so he's more interesting. I've gone through the tropes for heroes, but none of them stand out as particularly good for the setting (High Fantasy Wuxia, basically). Does anyone have methods to make sure that their protagonists aren't overshadowed by the other characters?