You use Benzin.
Here's some decent links for you to read. I advise you read them all and try to understand all that is being said. Then get a copy of benzin (You'll need to compile it yourself. There was a thread at wadder forums with binaries, but wadder forums are gone), download some legal base WADs (can be done with CustomizeMii), extract the brlan and brlyt files (again, use CustomizeMii), convert them to xmlan and xmlyt with Benzin, look at them, study them, work out how they work.
I advise you start with the WADder Base WAD 1/2/3, as they are quite simple animation, and so easy to understand.
Then, start writing your own xmlan and xmlyt files, and converting them with Benzin, then inserting them into channels with CustomizeMii.
Links:
http://wadder.net/wiki/index.php/Editing_Banners_with_Benzin
http://wadder.net/wiki/index.php/Brlyt_Documentation
http://wadder.net/wiki/index.php/Brlan_Documentation
Also, check out this file on the Benzin
SVN GIT, it lists all animation types, which is handy:
http://github.com/SquidMan/benzin/blob/master/animtypes.txt (Don't worry too much if this file makes no sense right now, it should later once you understand more about banner creation).
Alternatively, for a more "regular" animation (i.e. something akin to a GIF animation), check out this page:
http://wadder.net/wiki/index.php/Brlan_RLTP
And a helper for that :
http://spreadsheets.google.com/ccc?key=r3E...9jlbqfea-g2blcg
With this, you just make a bunch of images (like you would for a GIF animation), then convert them all to TPL. Then use the spreadsheet linked above to generate an XMLAN. For the xmlyt, see the WADder wiki page on Brlan_RLTP I linked above.
Hope some of this is of use to you.
EDIT: If this all seems a bit tricky (understandably so, because it is), you could always just use the Base WADs from CustomizeMii and replace the images (TPLs) in them. Just create new images in a regular format (e.g. png), and use CustomizeMii to replace the existing ones with them. It should resize your images and everything, so you don't need to worry about bannerbricks or anything. This way, you don't have to touch brlan or brlyt files. However, you are stuck with the animation in the original channel, you can only change the actual images.