Manual confirmation of user emails is no available as a standard feature, because it is not a legitimate practice. The email account owner absolutely has to confirm their email from their inbox. As an admin, you can resend confirmation emails, setup transaction email server to insure better deliverability and you can directly contact the email hosted to assist them with the confirmation process. 

There are situations when the email owner is known to the site operator, or the site operator may be receiving separate letters expressly confirming one's email ownership. In such cases the best thing to do is to resend a confirmation letter and send a personal note to the email owner asking them to confirm via a confirmation email. 

Opting-in emails manually may be illegal. Please, refer to https://www.ftc.gov/tips-advice/business-center/guidance/can-spam-act-compliance-guide-business - you may be fined for over $42,000 for EVERY email violation, and unless you have evidence of expressed record of email owner opting-in via Confirmation link from within their email, you may not be able to prove that your emails are sent legitimately.