My tutorial was exactly about this.
Let me sum it up in a nutshell.
When uploading sprites, hit the drop down box and find ATTR1, ATTR2, etc...
These correspond to the attributes at the right hand side of the gani editor. For example, ATTR1 (attribute 1) is the hat. Enter the image name in that box to set the attribute's image in graalshop.
You'll notice that they don't go further than 3 however. To extend this, open the gani in a .txt format and scroll down until you find 'DEFAULTATTR# <image>'.
Here's an example of the inside of Mythic Legend's idle gani:
NPC Code:
DEFAULTATTR1 ml_hattemplate.png
DEFAULTATTR2 ml_body-torso1.png
DEFAULTATTR3 ml_body-head1.png
DEFAULTATTR4 ml_body-arms1.png
DEFAULTATTR5 ml_body-legs1.png
DEFAULTATTR6 ml_armortemplate.png
DEFAULTATTR7 ml_body-arms1.png
DEFAULTATTR8 ml_body-legs1.png
DEFAULTATTR9 ml_shoetemplate.png
For a little info, do not use params for any gani that will setbackto another gani with that image. Params aren't meant to be permanent and do not transfer with setbacktos.