The /cwaypoint command lets you manage your waypoints.

/cwaypoint add <name> <pos> [<dimension>] [<color>]
/cwaypoint rename <name> <newname>
/cwaypoint edit <name> <pos> [<dimension>]
/cwaypoint setcolor <color>
/cwaypoint (remove|hide|show|get) <name>
/cwaypoint list [<current>]

• name is the name of the waypoint
• pos is the position of the waypoint (e. g. ~ ~ ~)
• dimension is the dimension the waypoint is in (e. g. minecraft:overworld)
• color is the hex code of the waypoint color (e. g. FF0000)
• current selects only waypoints within a world (true or false)