Once you added a place to bookmarks, expand the white panel and tap Edit bookmark. You can:
Choose or add new set (folder)
Change the color (tap red dot and choose your own color)
Tap double star symbol on the main panel to open bookmarks menu. Here you can see list of sets (folders) with bookmarks. Press the eye icon to hide certain groups on the map.
Here you can also edit pins or delete groups (folders) with pins.