if your branding feature applies the master page and any other resources, than at least you got that working out.
the stapler has two things you need to check:
- feature id: this should be exactly the ID attribute you will find in the feature.xml of the branding feature. don't confuse this with the solution id which the feature belongs to
- site template id. for my sites, this is particularly problematic because it depends if its the my site host, a personalisation site, regular my site, profile site, etc
my advice is check the webtemplate and the configuration properties of an existing SPWeb site object you are trying to associate, because together they form the id that the stapler needs for the association. odds are, the stapler is not associating with the right site template
edit: for obvious reasons, only newly created sites will be affected. just in case someone reading this is expecting an existing site to magically enable the branding feature