I forget where, but you can find a candle or torch somewhere that lights up those places. If you really want to try to play through it, you could always check gamefaqs.com. And yea, it is pretty damn confusing trying to figure out where to go and what to do in that game.

For zelda games there is also zeldadungeon.net

Twilight Princess IS after Majoras Mask in the Zelda-timeline after all

There is a real timeline. It splits into 3 alternate universes, though:

I'd assume Hyrule Warriors to be non-cannon, but who knows? Honestly, Nintendo could develop games in different timelines and it wouldn't really matter. No need to stick to one since they are split already.

Well, if you have played Ocarina of Time, it kinda makes sence. The first time child Link goes into the temple of time, he gets sealed in the temple untill he becomes an adult. Because the hero (Link) has been gone for such a long time, Ganondorf was able to destroy Hyrule. This is the "Hero is defeated" reality.
I don't really remember what happened in the storyline next, but eventually Link manages to defeat Ganondorf. Because he is an adult then who has missed most of his childhood, he gets send back in time to relive his childhood. This reality is then witouth link again (since he got send back in time), and this is the "Adult Era" reality.
The reality Link is sent to to relive his childhood is the "Child Era" reality.

The timeline does exist, however it's not the same link in all games. For example, in Twilight Princess, the Link from OoT/MM is supposedly dead (according to Game Theory he's already dead in MM actually).