Working out the kinks is an important step in combining video, stills and audio. The kinks would be your work flow, everything changes. My approach to how I shoot has changed drastically since I have committed to audio and video collection while shooting images.
My work flow at the moment goes like this.
In the field:
Set the audio recorder down in a safe place. Walk away to get rid of the camera shutter sound that will be picked up.
Shoot images, shoot video. I rarely use my Flip video for sound collection. Shoot images, shoot video.
Use a Holga to shoot vignetted macros.
In the office:
Using Image Ingester, download, duplicate and add keyword and copyright metadata to all media.
Using Photoshop edit Photos, HDR, Panos, Animations
Using Premiere rough cut the Video and sound. Save early, save often. Add still images and fine edit.
Transfer to permanent archive, duplicated and back-up on DVD-ROM.
I am certain that my work flow will become more efficient as I do this more.