You do this like this:
make a waypoint:
clear 5x5 area. build the waypoint shape outta cobble. place your signature blocks, right click center.. get the way point message. you should be able to now fill in all holes with dirt, if you want. you can hide the signature that way, but you may never remember it.. (like I did.. ugh)
go to your teleport initiation site
make a new waypoint like 2 blocks deep into the ground.
use a different signature on this one, fill it in
build a teleport rune on top of the waypoint so it's flush with ground. place your signature blocks of first waypoint, right click. Blocks disappear if working. you can then teleport to the first waypoint.
Now build a teleport rune on top of the first waypoint and use the signature blocks of the second waypoint. right click and test.
if all is done, fill in any gaps in your cobble stone runes with dirt.
if you fill a cobble stone rune with cobble, the rune fails.
The filler spaces have to be empty or a different material than the runes main body
the rune (waypoint or teleporter) can be built out of any single material you choose. I use cobblestone.