AFAIK you can't do that. You have to change the settings each time. About the only thing you could do would be to keep several Dolphin configuration files with a different controller profile in each one, then set up a script to copy and rename Dolphin's configuration file automatically to the one you want to use.
Sadly, there's no easy way to change memory cards, either. You have to manually edit Dolphin's configuration file or rename memory card files to switch between cards, too.
Sadly, there's no easy way to change memory cards, either. You have to manually edit Dolphin's configuration file or rename memory card files to switch between cards, too.