The Backup section of iExplorer is displaying the data within an iTunes backup on your computer. When you choose Load Backup Data (or 'Yes' in older versions) to make a backup in iExplorer or choose to Back Up Now, iExplorer creates a new iTunes backup for you. The article below explains how to avoid having this data overwritten by a new iTunes backup:
How to keep a safe backup with iExplorer
All other sections of iExplorer such as Media, Apps, Photos, Media Library, Books, and Root (with Jailbreak) are a direct connection to your iPhone or iPad and read the data directly from it without requiring an iTunes backup.