Applies to the 580EX II.
The 580EX was recommended to use a dummy battery in the gun to get the full benefit from the pack ~ was never an aficionado of that myself. The flash flattened its own batteries first but boosted by the pack.
The way I use mine, it's still moreorless the same way and I've found when I run out of juice, simply swap out the batteries from the pack to the gun an away you go again.
I rarely carry any spares! 
I've let it setup whatever way it came, happy out, so have not looked in detail, but the whilst I found the manual incorrect in practice for the 580EX it is configurable and works as stated in the manual for the 580EX II.
Edle wrote in post #4674729
Just curious but while using this CP-E4 pack, you still leave the batteries in your 580 EX flash right? It actually has access to all 12 AA batteries?