I don't really like writing stories where the main character buy perks. Typically they'll start with a bunch of perks selected from a variety of different docs and then get thrown into a setting.

So if I wrote a Harry Potter story where the guy has perks from other docs, it would start with him hanging around London looking for people. Evil Wizards, to be exact. He'd be hunting some before he goes to Hogwarts.

I get the idea for a character based on perks, and then think about what someone would do with them. How they'd handle a chain. How they'd behave. What impact their actions would have and what their long term goals are.

If it's a SI then it's even easier to write. You don't have to get into the mentality of an OC, you just write how you imagine you'd react to a situation.

I'd just keep a document on the side that lists all of his abilities and skills and also what he knows. It's a continuity document and reading it before I start writing and refering to it as I write keeps me from making any really silly mistakes or forgetting what his powers do.