Flash
(just kidding ... sort of)
What you are trying to do sounds like it is really pushing the limits of DHTML. Even if you do get it working on your development machine, it will fail (or at least, won't be smooth) for any user with a weaker computer. So if you want to get consistent smooth animation-following on all platforms, don't use DHTML; use a tool designed for it (like Flash, or maybe Silverlight if you're a .net person) instead.
However, if for some reason you want to go the DHTML route anyway (maybe all your users have bad ass PCs?), you're really going to need to explain how you are doing the animation. We can't read your mind and magically know what animation library you are using, so when you ask "How can you hook into the animate function" you need to specify what "the" animate function actually is.
**EDIT**
A commenter pointed out that you are probably using jQuery (because of your tag choice). In that case, you might want to look at this article I stumbled across this morning:
http://www.smashingmagazine.com/2009/02/20/ask-sm-css-smooth-page-scrolling-divs-of-equal-height-dealing-with-ie-6/
which deals specifically with smooth scrolling and jQuery.