Well it depends on who you want to write about or who will be in your story.

If you are going to write about before Yuri you'll want to know about Kanade.
If you are going to write on the alternate ending you'll want to figure out a plot on what Otonashi will do.

I recommend you write on Otonashi because he's the main character in the anime, you have more information on what he is doing (from the Another Epilogue), and I think the future is more interesting than the past.

Well what I planned and started is a new set of characters. I start out with one and on the 10th page I've written I introduced someone else. I don't plan on having them start a rebellion again anytime soon. Maybe just have them meet Otanashi.

I see. So this would be set much further into the story, after Otonashi is the only person left of the SSS. Right?

Otanashi is the student council president(like in the alt ending) and I guess you could say he is still in the SSS. I also wrote in one member of the guild who stayed behind and is scavenging around looking for things left behind by other members.

I think it would almost be easier to do it using Otonoshi because he is the main character. But, at the same time it would be cool to see something before Yuri came there that would be about Kanade (and maybe Naoi sense he was her assistant) so whatever you find more fun. ^^