You are most likely going to have to build your own custom login control. During first login, users will have to complete the 2nd factor authentication methods. Upon subsequent logins you will not require this.
In Kentico user table it stores the last logged on date/time. You could write your control to check for this value upon entering in username/password. If the value exists, you could code to skip the 2nd factor...if not then require that step.