The toolbar isn't really an appropriate place to store a large number of bookmarks - there's a limited amount of horizontal space. It's probably going to hold a maximum of 10-12 bookmarks, reasonably, provided you give each one a short name.
For example, by default, the name of each bookmark is set to the title of the website, which might look like "New York Times - Breaking News and Multimedia" - it's a lot better to just rename that to "NYTimes" for brevity.
So, to move some of those to the bookmarks menu, click the Show All Bookmarks menu as I mentioned above.
Then, click the "Bookmarks Toolbar" in the left side of the screen, like this:

On the right, you can select any of your bookmarks and rename them if need be. (Don't change the location, obviously.)
To move them to the Bookmarks menu, select them (you can select more than one at a time by holding down the command key and clicking each one), then drag the selected bookmarks to the Bookmarks Menu shortcut on the bottom left, and drop them there.
Now, if you actually click the Bookmarks menu again (at the very top of the screen) you'll see the moved bookmarks are now there instead of in the toolbar.
Hope that helps?
Matt