Photoshop Grouped layers into After Effects

A two-fold question really... I have a project with well over 50 layers... Half of those layers are placed in groups. And I've numbered and named them for AE's sake. When I import-file into AE (using retain layer sizes) and add the folder file to the blank composition - the layers firstly are scrambled out of order, so would like to find a better way to approach that... and more importantly, my layers are no longer in their groups but opened and scattered as well. How can I fix this?