How To Change Notification Preferences in Mac OS X El Capitan

Notification Center gives you a glimpse of the recent app activities and events that occurred on your Mac, and furthermore, it can be configured to sort notifications by time or group them by apps. 

Change the Order in Which Notifications Appear in the Notification Center

Click on the Apple menu > System Preferences > Notifications. Click on the drop down menu displayed next to Notifications Center sort order and then select the option that suits you best: 
- Recent: Sort notifications by time and display the most recent ones at the top of the list. Notifications older than 7 days are discarded. 

- Recents by App: Group notifications by apps, where the app with the most recent notification is listed first. 

- Manually by App: Group notifications by apps, but this time the notifications are displayed based on the order in which apps appear in the Notification preferences. You can change the order of your apps in the list by dragging them up or down. Remember to place your favorite ones at the top of the list.