A new bookmark is placed in the Unsorted Bookmarks Folder. From here, you can move any bookmark to wherever you want.

As to the "recently bookmarked" folder, do not delete from here.

Some information about so called smart bookmarks folders:

• "Most Visited" and "Recently Bookmarked" and "Recent Tags" are examples of so called Smart Bookmarks folders and are not real existing folders.
• Smart folders show a list created by a query of the places.sqlite database that stores bookmarks and history in Firefox.
• Smart folder lists show a maximum of 10 entries by default.
• Bookmarks and history items that show up in a smart folder list are stored elsewhere in another folder and any changes made are applied to the real bookmark or history item.
• If you remove an entry then the list is shifted up and a new entry that wasn't shown previously is added to show 10 entries.
• If you add a new bookmark or visit a website then a new item is added at the top and the entry at the bottom disappears from that list.
• Items that disappear from the list are not gone, but merely do not show up anymore in that list.
• Actions like copy & paste or delete that you perform on bookmarks in such a list are done on the original bookmark.