What do you mean by "customize"?
If you want to change the icon for a specifc bookmarked site in the Favorites list, then lizdance40 is correct. There is no way to change a site to use a custom icon.
If you want to change which bookmarked sites appear in the list, then the answer is yes, you can change the list of sites that appears in the list as well the order that they appear. To change which sites appear in the Favorites list, add bookmarks to or remove bookmarks from the Favorites folder by navigating to that folder in the Boomarks pop-over (tap the Bookmarks icon to the right of the address field, then tap the Bookmarks icon, then navigate to the Favorites folder, then tap the "Edit" button). You can also open a new tab, then press-and-hold on one icon to move it to a new location. Just drop it when it's in place.