It's designed so you can charge both phone and spare battery at the same time. Right from the product description:
Description
Charge your BlackBerry smartphone and an extra battery at the same time with the BlackBerry Battery Charger Bundle.Plug your BlackBerry device in to the battery charger - no extra cables required - ...
That said, I usually only charge both like that when I need two batteries to be 100% full in the morning. (That's usually if I anticipate being in a low signal area for a long day.) Usually I just charge the spare separately, use the one that's in the phone till it's low, then swap them. This way I'm never stuck with a dead battery.