Waypoints can be manually added to Atlas using the flag icon that appears on the menu bar at the bottom of the map window.
Touch the flag icon and a waypoint will drop on to the centre of the window or wherever the centre of your current location is if the location icon is turned on.
If you then move the waypoint (see below) it will not be locked to the position it is moved unless you go into the Waypoint editor screen, it will just end up moving back to the place you originally dropped it. So, as a precuation, after you have dropped a waypoint always go into the editor screen even if you are not actually intending to edit anything and this will lock it into the position to which you have moved it.
Waypoints can also be added from using the search field.
Waypoints can also be copied into the Points folder within Atlas when they are contained in a gpx or kml file. Please refer to the section on Importing Waypoints
To move the waypoint, hold your finger on it for a second and then drag it to the position you want to place it.
Tap the waypoint once and a bar will appear above the waypoint.

Click the x on the left side of the bar above the waypoint to remove the waypoint.
Click the arrow on the right side of the bar above the waypoint and it will take you to a Waypoint Details screen.

Here you can:

Once you have edited the fields you want to change, tap Done and then Save.
See section on Deleting