Welcome to the site!
I'm sort of in the same situation right now. I'm working on a scrapbook with my BF for his mom and we went through at least a thousand photos, more when you count the digital ones! We have at least 300 pictures sorted on my table right now.
We started by sorting them by kid, and then combinations of kids. We did keep the holidays out though.
I think when we actually start to scrap them its going to be somewhat organized chaos. Hopefully it ends up somewhat chronological. We found that there are just to many to sort into themes.
Good luck with your project, I can understand the major task you're getting yourself into!!