Firstly, you cannot just "spawn" waypoint (now I mean the yellow grid on game screen). There must be one already when the mission starts, it doesn't matter which one (move, seek & destroy, get in, ...).
I you want to switch the waypoint, for example when there is a waypoint "move" and you don't want to foce the player to get just to the waypoint, you can use this trick (my favorite
)
1) Create a waypoint for the player, which will be visible before you kill that guy. Set the WP type to "GUARD" - it won't change it's description to "WAIT FOR OTHERS", when you'll get close to it.
2) Create a trigger with condition you want to use for switch the waypoint (e.g. !(alive SoldierOne) or anything else). In the combobox where you choose type of the trigger (None, End #1, End #2 etc.) set "Switch"
3) Press F5 and synchronize that trigger with waypoint of point 1)
Then create the waypoint "MOVE" you want to use after the guy's dead.
That's it. Looks difficult, by this is because my not-at-all-prefect English and crappy ability to explain something