It’s very common to use Photoshop and Illustrator to prepare content for import into Adobe After Effects. Here are some practical tips to avoid problems when merging the software.
Import Tips

• Double-Click in the AE Project Window
• Shift-Click Multiple Items
• Organize in Folder and Option+Drag (Alt+Drag) from Desktop
• Keep file names less than 27 characters long

Photoshop

• Assign unique names to each layer
• Avoid using layer sets unless you want the layers to come in as a nested composition
• If layers are not needed, reduce your render burden by importing as a flattened file such as a PICT, TIFF or TARGA
• If you have applied an adjustment layer in Photoshop such as Levels, consider applying the effect directly to the individual layers in Photoshop instead

Illustrator

• Be sure to use layers in Adobe Illustrator to split up elements
• Change AI preferences to use AICB format (not PDF) for proper Copy/Paste