There's some documentation here: http://wiki.hard-light.net/index.php/Multimedia_Files#APNG
Let me know if anything in it isn't clear.
I got it to work, sure is a lot better than having thousands of dds files floating around in the mod.
I have another question, is there a way to make the dialog text in the top right larger? I've received a few complaints that the text is too small and hard to see when explosion effects are going on. I know voice overs kind of solve that problem but naturally I don't really have any voice actors.