Most of the beautiful backgrounds that you see in The Pirates! Band of Misfits are actual physical sets made of wood and plaster, so the matte painting team focused mostly on the gorgeous skies. A typical day in the matte painting department involved cloud-shaping in Photoshop.
See the video for a video montage of these images along with the snappy music from the film The Pirates! Band of Misfits
Here’s a nice article in The Hollywood Reporter about director Peter Lord and The Pirates! Band of Misfits at the Oscars.