New to AE 6 is the ability to distinguish when importing a composition as cropped layers or a composition. Previous versions always chose to crop a layer based on its content's boundaries.
Importing with cropped layers is useful if you will be rotating, scaling, or animating from the anchor point of a layer.
Cropped layers place the anchor point in the center of the information of that layer. As long as your layer has equal parameters, you're golden.
You can always move your anchor point though so don't fret. Select the layer, choose the pan behind tool from the tools palette, and click on the anchor point to move it. This works from the composition window or layer window.
Import as a composition if you want the layer's content to have identical dimensions and anchor points.
Import as a composition if the filters you are using tend to get ˜chopped at image boundaries. Some older effects and third-party filters cannot draw beyond an object's boundaries.