They work with regions.
Although you may think they teleport you from one Waygate to another, they don't. They teleport you from the waygate, to a region.
If you want it to teleport to another waygate, simply place a region and put a waygate on top of it.
To set where you want it to teleport you, just double-click the waygate in the terrain editor and it'll open the specific unit's properties, of which you can set it's teleport point.