I created a waypoint that I didn't mean too

[IsLegitimate]

How do I remove waypoints and rename them and change the image that goes with them?

[MehVahdJukaar]

to remove shift click their bookmark. to change their texture you'll need a texture pack that retextures them. You cant rename them. Only delete them and place them again with a new name. You can also add entirely new waypoints (map markers). Follow the supplementaries wiki, its explained there