By makeing certain spots on the sprites to label a different color thats looks the same as it's original.
Then for the alternate costume, you change the altered colors(and old) to match your new look.
Or something that uses way more space:
Get your sprites loaded, and then add another costumed set of sprites.
Then give them each their own animations, and then in each of their states, make a code of
[state 0, Costume 2]
type = ChangAnim
value = ;The new animation
trigger1 = PalNo = 1 ;2 -- 12