Problems setting ONLY waypoints

Hello, we have 2 (submarine) Blue ROVs working with groundcontrol. We encounter two big problems and we need to solve them to work properly with our surveys.
The first problem, is that we can not draw single waypoints, because when we draw them, the software creates a line, and the waypoints dissapear. We haven´t found the way to create only waypoints, on the screen, because we use the waypoins to identify points to make inspections. How can we plan inspections waypoints for our ROV inspection surveys?.
Another problem that we haven´t found an easy solution is to upload a dxf with waypoints or a dxf map to plan our works. What is the easiest way to do it?.

what software u r using ? if use ros, u can send the waypoint msg to the robot.