Hello Andreas,
These are two separate folders and should not be placed as one.
Favorites in the navigation pane is actually your C:\Users\(user-name)\Links folder, and is for your favorite shortcut "links" to use while in Windows Explorer.
Favorites in Internet Explorer is your C:\Users\(user-name)\Favorites folder, and is for your favorite website shortcuts to use while in Internet Explorer.
Hope this helps,
Shawn