Skyportals are nothing else than another, smaller, skybox with a _skybox (or misc_skyportal) entity in it. The big advantage of skyportals is that you can put everything you want into the portal and those things will get projected into the normal skybox. That allows you to add special effects such as additional suns/planets but also a terrain or buildings into the skybox without editing the images.
As already said, the skyportal is a second skybox in your map. It is important that it is not inside of your normal map geometry. That means you have to place it separately so that it wont come into contact with any other brushwork of your map. Once you did that, you place the _skybox (or misc_skyportal) into the second skybox. If you cannot select this entity in Radiant, add the following lines at the end of your entity definition:
/*QUAKED _skybox (0.77 0.88 1.0) (-4 -4 -4) (4 4 4) -------- KEYS -------- "angle" : rotation angle of the sky surfaces. "angles" : Individual control of PITCH, YAW, and ROLL (default 0 0 0). "_scale" : scaling factor (default 64), good values are between 50 and 300, depending on the map. -------- SPAWNFLAGS -------- (none) -------- NOTES -------- Compiler-only entity that specifies the origin of a skybox (a wholly contained, separate area of the map), similar to some games' portal skies. When compiled with Q3Map2, the skybox surfaces will be visible from any place where sky is normally visible. It will cast shadows on the normal parts of the map, and can be used with cloud layers and other effects. */