Using all BOokmarks features in safari, how please?

From i learn computer, i did not depend or trust the bookmarks on any browser, without reasons, and each time i need to save a wetsite, i put it's link in a txt file.
But i discovered that i lost many things, i need to use this.
i know that CMD+D can save any site in favorites, but if i do not want to save in favorite, what can i do? and, how can i arrange delete or anyting from favorites.