To change the destination portal: When you open Map Maker look for the words "Destination Position." Then create an object (maybe a fern or something you can run through) and put it where you want the player to appear. Then copy the X, Y, and Z values/numbers of the fern (y`know, the numbers in the boxes right next to X, Y, and Z that aren`t used for changing size?) to the X, Y, and Z boxes of the "Destination Position" part of the "Map" tab. Then delete the fern if ya want.
Maybe you could try making a terrain height map / height map for your next map.