Okay. Let's assume a simple one-way transition using a trigger and a waypoint. You draw the area transition trigger somewhere, and it will be visible and clickable in the game as a blue zone. You put the waypoint in some other place, so that when you click the trigger in the game, you are teleported directly to the centre of the waypoint, looking in the direction of the waypoint's arrow.
You can link the two very easily. Just change the waypoint's tag, this is done under Properties -> Basic. In the middle box, named 'Tag', enter a new name. Call it 'transitionWP1" for example.
Then, under the trigger's Properties -> Area Transition tab, select 'waypoint' as the destination type, and enter "transitionWP1" in the Destination Tag box.
That is all.
As to where you should place them, the two most common methods are either drawing the waypoint around a shape on the ground, like a sewer grate, a rug, portal or similar, or placing a square or trapezoid shape along the edge of a map, usually but not necessarily on the middle of a road.
Waypoints can be placed anywhere. Sometimes you'll want to place a magic circle on the ground with the waypoint in the middle, or perhaps you want to place the waypoint in a doorway. Placing it near the edge of a map in the middle of a corridor will also work.
If you are using a two-way area transition, waypoints are often placed at the centre of both triggers.
If you can't get it right, try experimenting so you can locate the reason behind the not working (you may have entered the tag in the name box, misspelled the tag, put capital letters in the wrong places, there can be lots of causes).
Again, hope it helps. A module without transitions is often severely handicapped
