To set this up for your Brawl mod, open this file up in BrawlBox.

Go to section 8, and rename 3F to the ID of your Bowser clone and
40 to the ID of your Giga Bowser clone.

By the way, this is the "ft_koopa-gkoopa BX v1.1" rel file.

Also, this is the rel file your Giga Bowser clone will load.
See how to set that up in the FighterConfig's Note text file.
It's actually quite simple.