Meanwhile over in Hyrule B we know that Link suddenly dissapeard and the Hero of time vanished into legend (we get that story at the beginning of Wind Waker) Sometime after OoT Gannon escaped his prison and waged war again on Hyrule. the people waited for the return of the Hero of Time but he never came and in the end the world was flooded and we arrive in the world of Wind Waker (GCN).
Now I am only half-way through TP so I haven't finished the storyline yet (and am desperately trying to avoid spoilers) but the word on the street is that it happens in Hyrule B between OoT and Wind Waker, and I know that Phantom Hourglass (DS) that's due out next year is a direct sequel to Wind Waker with the same young Link. That only leaves the two Oracle games to fit into the timelines.
The Video supposes that they both happen at the exact same time in different Hyrules and both at the respective end of the timelines, with the whole world being "reset" as it were.
So that's the basic premise behind the split timeline theory as to where everything fits. Much of this is speculation. What can be confirmed though is the following.
1. Before the Minish Cap was produced, OoT was confirmed as the First game in the timeline.
2. Zelda II is a direct sequel to Zelda I
3. Two different Hyrules were created at the end of OoT (confirmed by Miyamoto at the announcemnet of Wind Waker)
4. Wind waker is part of Hyrule B
5. Phantom Hourglass is a direct Sequel to Wind Waker
6. Majora's Mask is a direct sequel to OoT
All of this does allow for different variations on the timeline, but the one presented in the video from Gametrailers does seem to make a lot of sense to me.
I hope that was helpful.