Sync footage with alpha to audio

Here is a situation.
You have a gun muzzle flash clip (or any other pre-keyed footage) and you want to sync it with an audio file such as a gunshot sound.
Since this clip would, by nessessity, be above the primary storyline, Is there any way to link this clip to the SFX so you can move one and not lose sync without losing the alpha channel when creating a compound clip.
P.s. When all this emthesis on linking and making connections, wouldn't it be smart to allow clips to link to each other rather then always linking to the primary storyline. What if i want to move a whole bounch of titles and audio over another clip? What if you want a clip on the secondary story to link to a song cue?

Hi Shane,
Thanks for your help.
Yes, recorded on the tape the vision is about 2 sec behind the audio and also EE through the VT machine if just playing the timeline [which is in sync on the computer].
I am not supplying a reference to the deck. As I mentioned I have used exactly this set up with the same machine and FCP set up without these problems working in PAL about 3 or 4 weeks ago. I also made a DVD of one of the edits and that is in sync. I am thinking it's either something in the Kona 3 - but the problem should be apparent when monitoring it - or in the VT machine. The reference was something I had thought about but I don't know enough about that side of things....
peter

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