You can color-code each item on your Bookshelf, and "filter" your view of the Bookshelf to only show items of one color at a time.
To do this, tap the color palette at the upper left of the screen, and choose the color you want to show. The currently selected color will have a green checkmark. Choose the white color at the far left of the list to show all items.
Regardless of what color is selected, your Bookshelf will automatically sort itself so the items you open most often come first. Let us know if you would like other sorting options, for example alphabetically, or by date added, or manually.