This is probably the most important step. While all your graphics are on one layer currently, you need to group each set of graphics that you would like to be separated onto it’s own layer. Each color here are in separate groups.
With your layer selected (the objects don’t need to be) toggle down to “release so layers (sequence)” from the Layers dropdown.
Now in After Effects import your .ai file, it’s important you chose “Composition- retain layer sizes” under the “Import As” dropdown. That way all your anchor points are center to each individual layer and not all center to the document itself. And if you choose “Footage” then your file will import as a flat graphic on one single layer.