Howdy,
Expression Encoder is a post production video editing tool that you use to setup your video as required.
If you are looking at over laying or creating animations for video, there are applications specifically created for that which "render" projects into the file formats you need. You can then take those file formats into Expression Encoder. You may want to look at applications such as 3D Studio Max for instance.
Expression Blend is not an application for authouring Video Animations. It is used for application and web site technology development.
HTH
Cheers
Expression MVP
my blog : http://x-coders.com/blogs/sneaky/default.aspx