Well, part of the fun (and challenge) of any RPG is figuring this information out (and figuring out how to organize it) for yourself. That said, if you have a more specific question there are four things I do:
1.
The Compendium Encyclopedia. The creators of the Compendium have done an amazing job with it.
2.
GameFAQs. Here you will also find a lot of information, including several step-by-step walkthroughs of varying quality for each Chrono game.
3. Browse these forums to see if your question has already been addressed. This is a very good Chrono community, and most people here are more than willing to help, but having 100 people ask the same question is silly.
4. Post your question for all to see. You will get more replies than you could ever wish for, and <sarcasm>if you cross your fingers your topic might just get hijacked and taken in a completely different direction</sarcasm>.
In response to your question:
How do you keep track of everything?
I use pencil and paper.