A waypoint is just a location to move to. If you say 'Move to X, Y' and enter a coordinate the other side of the map, obviously the unit tries to reach that coordinate. If you say 'Add waypoint at <position other side of map>, Add waypoint at <original position>' then the unit goes to both waypoints, in order. It'll go to the other side of the map, then come back to its original position.
As for units moving over each other - use 'Avoid moving over object' action on start of layout. The RTS basics template has an example of this. Units will negotiate in to a queue and not overlap too much.
It's not perfect though and I've been planning on improving it, especially since it's annoyingly easy to set up parameters that make them spin around in a dumb way, and you have to tweak the parameters at the moment to get it to work right. Hopefully I can come up with a better engine. It's really tricky stuff though.