Well, if you want your waygate to be active the whole time, then it is simple.
1) Make a region, which will be the destination point (= where units, which enter Waygate, are teleported). Regions are created via the "Region Pallete" panel - R key by default.
2) Find Waygate unit (it's under Neutral Passive player) and place it where you want it.
3) Select the Waygate you placed in your map, press "Enter" key -> unit specifics window will open.
4) In the window, there is a checkbox with "Way Gate active" - check that box and select the region which is the destination point.
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If you want to activate the way gate later ingame, there are 2 ways to do this, but both require triggers (albeit those are simple).
You can also deactivate the way gate via triggers.
If needed, I can post those triggers.