Link shows up in your game when you play it and you use the zelda-w program to play.
When you want link to start on a certain screen, go to Quest-Dmap Data-The first you see(probably 0).
The type the number of the screen you want link to start at Continue: 0x(type your number).
If it's on a other map, change the map number to the number it has to be, but I guess you don't need to make a change to that.
Example:
HereNow go to the starting screen to set the certain spot, link needs to be. Scroll around on the work bar on the bottom until you see some sort of stairs, a green and blue warp, a rupee and a flag next to each other.
Click the green warp and set it on the spot where Link needs to start.
To make warps, place a tile(also named combo) with the properties of stairs, direct warp, or the cave stuff where you want. Now go to Data-Tilewarp to set the properties, it's alot like the stuff about the starting screen I told ya before.
Erasing the black outlines? Make sure the pixels are black with a X trough it, and if you want people to walk under the treetops, use layer 3, not 2.