You need to import the document as a composition to get access to the individual layers.
See this page for information on preparing files in Illustrator: "Preparing and importing Illustrator files"
See this page for information about importing layered still images as compositions: "Importing a still image as a composition"
@speakeasy11, apparently, you cannot import 'sub' layers as separate objects, you have to convert all 'sub' layers to regular layers by using the "release to layers" command in illustrator. Then, you have to pull all the newly converted layers to top-level layers. Have a look here http://aftereffects.digitalmedianet.com/articles/viewarticle.jsp?id=30923-0&afterinter=tru e
you cannot import 'sub' layers as separate objects, you have to convert all 'sub' layers to regular layers by using the "release to layers" command in illustrator.
Check your terminology! You are only confusing the OP. There are no sub-layers, only objects in an EPS file. You're right about the Release to Layers, though. it would be the easiest way to get every object onto a separate layer.
well, whatever terminolgy you use, here is a screen shot of an eps file in illustrator which is likely what the original poster is seeing with his file http://testbeforelaunch.com/temp/eps.jpg the "objects" or more appropriety "paths", as mentioned before must be "released to layers"