You can click the yellow pill button in the upper left corner of a window to minimize an app’s window in macOS Sierra. However, if you minimize a lot of windows, the right side of the Dock quickly becomes cluttered. The solution: minimize windows into their app icons.
If you enable this feature in Dock Preferences it shrinks all minimized windows into their app’s icon application icon instead of into the Dock. Open System Preferences from the Apple menu and choose “Dock.” Check the box next to “Minimize windows into application icon.”
If you have a lot of minimized app windows, and have trouble finding what you’re looking for, control-clic) the app icon to reveal a list of that apps minimized windows. Choose an item from the list and it will open.