Jpcsp will auto detect the profiles and use them (the settings page in jpcsp should be greyed out when the game is running off a profile, otherwise it will use the default settings)
So basically Jpcsp has two settings one global (the one you will see in the launcher and jpcsp all the time, and a profile for the game, the only way to tell its using a profile is if the configuration page is all disabled in jpcsp.)
You can re-load a previous profile back in the launcher by selecting it in the pull-down at the bottom right, then click Load, re-make any changes you need then re-save the profile or the settings will be lost.
example of jpcsp running on a game profile
btw this feature is still experimental in both the launcher and i'm sure jpcsp
So basically Jpcsp has two settings one global (the one you will see in the launcher and jpcsp all the time, and a profile for the game, the only way to tell its using a profile is if the configuration page is all disabled in jpcsp.)
You can re-load a previous profile back in the launcher by selecting it in the pull-down at the bottom right, then click Load, re-make any changes you need then re-save the profile or the settings will be lost.
example of jpcsp running on a game profile
btw this feature is still experimental in both the launcher and i'm sure jpcsp