When the player is within the transition area, it is possible to trigger a changelevel. You do not need this brush based ent in most situations. However, I found that lots of stuff might follow you through a changelevel, that you dont want to, without one. Therefore, if you use a script with a generic monster, as an example near a change level ending, then set up a transition ent that does not cover the area that the generic ent is in, but covers the area the player will be in. Then the changelevel will only take the player into the next level.
Lets use some short names for the entities.
We wont bother with the transition brush. You probably wont need it. If you do its placement is not important apart from the fact that you must be in it for the change level to work. This picture is from autolycus . It was intended to show how to setup a seamless change.