Welcome to Android Central! You don't have to have all apps on your homescreen--think of it as similar to the Windows 7 desktop, where you can choose which programs to place a shortcut of on the desktop, while every single program is still available in the All Programs list. In Android, you can see all apps in the App Drawer, and select which ones you want to add a shortcut to on the homescreen.
You can also create folders on your homescreen to reduce clutter:
How to create folders on you Samsung Galaxy s3