1). Play all games. Let me say that again: PLAY ALL GAMES. Play them many times, because you will pick up something new with each play through. Most of y'all are in school (high school or college) so you have plenty of time to do this. Trust me, once job, marriage and kids enter your life you'll only have time to play the hand helds while on the toilet, so I haven't played TP as much as I'd like. I just hate seeing 'i haven't played this game yet, but this is where I think it goes' right before yet another theory that will get shot down in 5 min by Lex, Pinecove or CP. So play the games, please.
2) Kind of goes along with the first, read all dev quotes that you can. This one is alittle tougher, cause most quoted are translated from the Japanese, so their accuracy is sometimes in question, and devs aren't always right. Dev quotes can't be reviewed objectively like games can be, either, because they are obviously open to interpretation. At any rate at least make an effort to go to the relevent sticky thread at the top of the Theorizing page right here on ZU.
3) similar to translated dev quoted, it might by useful to read the retranslations of the Japanese games and manuals. The relevent links are listed in another sticky thread at the top of the theorizing page. Some people have made the arguement that the original Japanese is more accurate than the NoA translations the western market gets.
4) try not to duplicate a timeline that has been posted recently. Read up on some of the previous posts and note the timelines that others have postulated.
That's about it, except that I think most timelines can do with some 'crazy' in them. Thinking outside the box is important because theorists having been throwing timelines at each other for years and years, and I've been trying to figure out a timeline ever since ALttP-- LoZ/AoL just didn't seem 'quite right', so I've tried alot of different ideas over the years. The most important thing I discovered is that no timeline will be perfect, and every theorist needs to use at least some fan fic. If you think your timeline is flawless, think again, because there's plenty of people on this board who will gladly poke holes in it.