All the photos you've selected to use in your project appear in the photo well (see example). Any photo that has already been used in the project has a blue check mark on it. If you remove a photo from your project, it is unchecked in the well, indicating that it is not used in the book, calendar or other product. For example, the right photo in the 2nd row is unchecked in the example. You can select HIDE USED PHOTOS from the Options menu in the well to show only the photos you haven't used.
To remove a photo from the well (and the project), click the "X" on the photo in the well. If the photo is in use, you'll be prompted to first remove it from the page where it is used. If it is not being used it will be removed from the project, but not from your library.
The other option is to restart your project, which removes all the photos, embellishments, design and other changes from your project pages but keeps the photos in the well.