Name your layers in Photoshop and Illustrator! Be organized, stay organized. You'd rather animate "small green circle" than anonymous "Layer 43." You can name layers in After Effects but you have to go through each one and remember what's in them. Naming layers properly in the external application also helps After Effects find lost footage faster.
Choose descriptive and varying names .
Don't make names too long.
Avoid using alternate symbols such as { ^ etc. as there may be cross platform compatibility. It's also a good idea to position layers as you want to find them in AE.