Ok, in Safari there are 2 main Bookmark storage places, the Bookmarks Bar and the plain old Bookmarks.
Bookmarks can be opened, by clicking the open book icon and then your bookmark. But if you wanted to have your bookmarks appear in the bookmarks bar, either edit your current bookmarks or add them again.
To edit, select the open book icon, click edit, click on your desired bookmark, then touch the third option, where it says "Bookmarks" and instead select Bookmarks Bar.
When ever you add a new bookmark, just make sure to save it in Bookmarks Bar and not in Bookmarks.