No change - AE only uses top-level layers.
What do you mean 'top level layers' ? I have to merge the illustrator document, correct ? Maybe I should go with a flash type program for this project.
Top Level Layers refers to the fact that you can have groups in layers and many different folder levels inside a layer in Illustrator. After Effects sees only the top level of layers. You can have 100 different groups inside a main layer and AE will see them all as part of one layer. However, if they're all top level layers, AE will see 100 different layers. Illustrator has a handy Release to Layers command that you can use to make the layers you need.
...so in other words, use the New Layer button in Illustrator, put your group in it, and life is good.
You may observe some unwanted interactions between the layers in Illustrator -- one layer blocks the layer below it, for example -- but guess what? You'd have to deal with the exact same thing in AE! Solve those problems in Illustrator.