If so, just put the video of the audio into the animation

Can you add video to the animation program?

Unfortunately, I'm not up on 3D programs, though I'd recommend doing a google search to see if you can find forums devoted to those programs where audio maybe discussed. It's possible that the programs don't support audio and it must be added in a video editting program after you've completed a clip or put all the sequences together. This would make syncing audio to character's mouths complex but it would be inline with what traditional animation had to face over the years. How that is done can be researched if necessary. Audio is usually recorded first.

@Boom, I use 3Ds Max, or 3D Studios Max. I've found some tutorials, but their not very detailed on where things are the program, as in where to find the audio controls, as such.

Which program are you using? Most should have at the very least a sound track channel and some have a drag and drop feature to add dialogue to particular characters.