Once you added a place to bookmarks, tap the bookmark on the map → expand the place page and tap "Edit bookmark". You can:
Choose or add new set (folder)
Change the color (tap red dot and choose your own color)
Tap the double star symbol on the main panel to open bookmarks menu. Here you can see list of sets (folders) with bookmarks. Uncheck the box to hide certain groups on the map or tap "Hide All" button to hide all lists on the map.