The archives will group all 3 stories together. You're going to want to create a save file for each character, this way you can go back and complete each story as you wish. Also, you will be prompted at the end of your 3rd story (whoever that ends up being) to create a new save file for the final episode. So, you'll end up with 4 save files total: 1 for each character, and one for the final episode.
All the info from each story though will be grouped together in the archives. So no worries about that. I'm assuming the game updates the archives as you go through. I'm not 100% sure on that though. I can't say that I checked the archives regularly as I went through the game. I checked them out when they first became available, and then again when I was done all 3 stories. Kinda neat to see how all the events line up with each other, and see who went to each world first, at least in my opinion. Hope this answered your question. If not, I'll be happy to give it another shot
Trust me on this. I've finished the game already. The archives will fill in properly if you have a separate save file for each character. I'm now just trying to get 100% on them all, which is by no means an easy task for this game. And if I may suggest, save Aqua for your last character. The progression of all 3 stories seems to flow from Terra to Ven to Aqua. Enjoy the game!!