Does it not show up?
that because the green thing and the bit that actually teleports you are two different things, just placed well together.
Heres how to be able to see your teleporters:
ok, for this example we're using Blood gulch.
1.)make a new teleport pair
2.)position them to where you want, in this case,from the bottom of the base to the top making sure the one that teleports you is facing into the wall:

3.)Now select a piece of nearby scenery, and duplicate it, lets use the nearby rock, for example.
4.)on the right, click the arrow next to 'swap' and select 'scenery\teleporter_shield\teleporter'. it should now look something like this:

5.)now move the teleporter on top of the bottom teleporter,and rotate it to match, like this:

6.) now, duplicate the 'teleporter_shield' that you have selected, and swap it for 'scenery\teleporter_base\teleporter_base' and on the right click 'Set Rotation(s) to Zero' and it will flatten it so that it is level:

7.)now move that on top of you other teleporter part, and its done!
you can do this anywhere, as long as the teleporter_shield and the part one of your pair is aligned properly, it will look like you teleport when you hit it, heres a screen of one in my mod:

DO YOU WANT A TWO WAY TELEPORTER?
ok, its easy.
1.)follow the steps for the one above
2.)the make a new teleport pair, and position part one with part two of the old one, and part 2 with part one of the old one
3.)then add another shield to your first destination, so there are two,
4.)DONE, wasnt that hard was it?
Id post a vid but for some reason it flickers when i play it back...