It sounds like your son already has his own Origin account with BF3 on that account so the easiest way would be to create a seperate user account on your local machine for your son where he can log in and sign into Origin with his own credentials so everything is kept neatly seperate. If you don't wish to create another user account on your machine you can have your son simply log your account out of the Origin client and sign in with his own Origin account on your computer's main user account. When you wish to play you can log his account out of the Origin account and sign in with your Origin account.
As stated if your son doens't already have BF3 he'll need to purchase a copy to use on the second Origin account.