Although many people like the feature that lots of panniers come with only one large pocket for carrying everything, it is hard to organize these bags. Finding small items within them can be difficult, and at times frustrating.
One great solution to this problem is organizing your things inside smaller bags within your pannier. Small ditty bags or even gallon-sized zip-lock bags work great for this task. Another added benefit to organizing this way is greater protection in the case of rain. Also if you have a fully waterproof bag, sometimes water can still get in if you are riding through a torrential downpour. Placing essential items such as your wallet and phone in a smaller waterproof bag within your pannier will stop them from getting wet even if there is a leak.