You can prompt an applicant to complete information for their spouse or partner and separate that data in the 2nd person's CRM profile. Follow these steps to setup the application:
Setup the forms you would like to include in the application flow. When setting up the form for the spouse/partner, make sure you select the box Generate a new CRM record when completed in order to generate their CRM record.
Make sure that all your spouse/partner questions are on the single form noted with Generate a new CRM record....
Assign the forms to the application. We recommend adding the spouse/partner form to the end.
Now when your applicant completes the application, the CRM will setup the records appropriately by linking the two CRM records, completing the application on the main person and ensuring the attributes were tagged to the new CRM profile generated.