So I create a wav file in Soundbooth from a sync mp4 audio file. Is there a way to keep the newly created wav file in sync with video on the timeline in CS4?

Hi. I presume you mean locking them together? Select both tracks and right click on them - there is an option to group tracks in the drop-down menu. Be aware that if you want to add effects you will have to ungroup them, add the effect and regroup them. Hope that helps.