If I’m not mistaken on the Helix, if u press the menu button once, it gives you the option to clear the current tracks which are the red lines.
The waypoints will have to be exported from the head unit and installed on the Autochart program separately. The ZEroline card keeps only the mapping info and the waypoints are stored on the head unit. That’s way the waypoints show up on the screen with navionics or lakemaster cards when installed.