Currently there is no way to synchronize videos with
animations as is possible with audio.
You might like to distribute the content of your slides over
multiple slides to have an effect of animation. Morever, set
'advance by user' option for each slide, so that the slides just
don't keep on playing automatically.
Once you have things on multiple slides, you can put THV
according to the content of the slide.
To do that you would have to split your flv file into
multiple parts (if you have Presenter 6).
On the other hand, in Presenter 7 you can just add the same
file on each slide and then adjust the time in Video Effects. BTW,
if you choose this route the published content would be bigger than
required. But, there is a manual post-publish work-around to handle
that. You can open up <publish path>/data/viewer.xml in some
text editor. Locate the flv file reference for THV on each slide.
Change the url of these THV to be same (say to be same as that on
slide1). Then go to the published resource folder and remove the
flv files which are no longer being refered to from
viewer.xml.