Does wife have her own credit card accounts or just "extra cards" on your account? AFAIK all of the miles from a joint account would go to the primary account holder's FF account but if you have different accounts, both Jane Smith's own spending and John Smith's spending cannot be credited to the same FF account in John Smith's name.

BTW, she should have some of her own accounts to clearly establish her own credit history and in case something happens to you.