1. Choose the action you need
Bend pushes plants aside. Cut makes them shorter. Destroy hides or collapses them, and Regrow brings them back. To actually add a plant, use Place; to remove a planted crop, use Harvest.
2. Prepare for Play
When Unity asks to prepare Runtime Data, let it finish. Runtime Data is a faster-to-load copy built from your plants and settings. Streaming then loads the parts near the camera without deleting the saved plants farther away.
3. Change the scene from your scripts
You can change tint, wind and shadows during Play, or add and remove plants. Paint Density, Noise, Color and Placement Mask while Play is stopped; these maps cannot be repainted during gameplay.
4. Test the result
Try a Player build as well as Play Mode. Move the camera around the map, plant and remove a few plants, and check the result after leaving and returning to the scene.
Runtime example
VegetationAPI.SetGlobalTimeOfDay(area, 17.5f);
VegetationMutationResult placed = VegetationAPI.PlaceWithFeedback(area, spawnPoint, typeIndex, seed);
Debug.Log($"Placed {placed.affectedCount}");