Floof, this brings in the Game Help section, for future record~
But anyway, it sounds like you're having issues with the arrival coordinates.
Let's say you're connecting Map1 to Map2.
You already have the Cape portal in Map1, so you place a portal in another part of Map1 that will go to Map2. So here's what you're gonna do:
1.) Grab a pencil and paper, and open up Map2.
2.) Bring your screen in Map Maker so it's facing the direction you want your character to land, where you want the portal (as if your character were in-game, in front of you).
3.) Place your mouse exactly where you want your character to land, and look at the X, Y, Z, and Yaw coordinates at the bottom of your screen, and write these down (Don't move your mouse!)
4.) Go to Map1, then place your portal where you'd like. You'll see a place for coordinates (X, Y, Z, Yaw), and here you'll type in the coordinates you previously write down.
5.) Save, and test your map. All should be well for you. c:
I hope this fixes it!