When you record sound separately with the 5d you need to sync it with the video in post. Normally you do it manually with a clapperboard and match the audio spikes.
With Final Cut Pro and plug in pluraleyes from singularsoftware.com you don't have to do it manually anymore. it's all automated and saves you a stack of time.
Singular didn't ask me to make this, I just had such a great experience with this software that I wanted to share it with you.