Please use a clean rom, for the sake of reducing potential user errors. Some steps will vary if you've already added scenes or routes to the game, for example.

Because we want the added scene linked into OoT's existing overworld, you're going to need this modified scene. In guide-res-scenes.zip, open the sub-folder named 91. Copy its contents into the sub-folder 91 in the scene directory of a dumped rom filesystem.

This is to update the Lost Woods so one of the exits will take you to the custom scene we'll be testing. Otherwise, we wouldn't have a way to get to the custom scene in-game. An already-modified file has been provided because the process involved is beyond the scope of this tutorial.

Now copy the sub-folder named 110 from guides-res-scenes.zip to the scene directory of the same dumped rom filesystem. This is our custom area.

Finally, the route table needs a new route added that will take us to our custom scene. Open route.txt (located in the dumped rom filesystem) in Notepad++. Scroll to the bottom, and paste these contents:

What this does is make it so exit 1556 (or 0x0614 in hex) warps Link to the scene in folder 110. The spawn point (entrance) used in the scene is 0. The "extras" are there to account for night, and Adult Link.

Please refer to the zzromtool manual for a more in-depth explanation of how route.txt works.

Don't forget to save.

Now build the rom and enter the Lost Woods from Kokiri Forest. If you keep walking forward and go through the log that normally takes you back to Kokiri Forest, you'll find yourself in our added scene, without any existing scene having to be replaced. If you exit the custom scene, Link is spawned in the appropriate place in the Lost Woods.