To set this up for your Brawl mod, you need to rename 
the name of KOOPA to what your Bowser clone character
is and rename GKOOPA to what your Giga Bowser clone
character is.

Next, make sure "Merge Motion/Etc" is checkmarked
for both clones.

Finally, open up the Giga Bowser clones's Fighter
Config. scroll to where it says the module file.
For example, "ft_gkoopa" or "ft_giga mac" if you
were cloning Giga Mac. Rename this part to the 
name of the rel file for your Bowser clone. For
example, "ft_koopa" or "ft_little mac".