This is not recommended at all, but the solution i used was to copy
the LAYOUTS folder in the 12 hive to a new folder, change the setting
of the _layouts virtual directory in IIS to point to the new folder
and edited the application.master in there. You cannot change
settings to point to a new master, it has to be called
application.master. You need to be careful that all the required
ContentPlaceholders are in place or things will break.