Arrgh... finally one I know, and I can't get access to my arcade machine to pull it.
I fought with it for a while, but then I found a fairly easy and quick way to do it.
I can't remeber the exact specifics, so the general gist is:
Get dafreaks Zinc GUI with the winterblast plugin:
http://dafreak.emuhq.com/it overwrites the default controller.znc with winterblasts.
Then launch it, and use the key configuration utility to setup the controls the way you want for your other frontend or controller(in my case it was Gameex)
It will create a new controller.cfg file, then in my case for gameex, I simply specify in the launch options --use-controller-cfg-file=d:\zinc\controller.cfg
It'll then use your created config template.
This is the way I created it this time, before i knew of winterblasts new controller.znc I created it by hand, I have that file here to if your interested, it uses zinc's default controller.znc. All you need to do is enter the appropriate key codes into the controller.cfg file and launch it the same as above.
Let me know if this helps!
Sound Doc
(edit I used Dafreaks gui, not Aldo's this time, much easier....)