AES algorithms - in any mode - are designed to encrypt binary data. The output is binary data as well, although the implementation may choose to convert that to any format. That your GIF is multi-layer is of no consequence to the AES algorithm - as long as it is fed binary data it will encrypt.
Decryption works the same way. Unless you are taking the GIF apart, the entire image will be encrypted/decrypted - including any layers.
Steganography is hiding data in - for instance - an image. This is not the same as just performing the AES block cipher. Normally you cannot just encrypt an image and include that - the encrypted image is just random data - if you try and read a GIF format from just random data it is likely that your GIF parsing will fail.