Use the deeplink module for that. After signup send out a mail with the verification link. This link is a deeplink that you use. The microflow picks up the parameter to retrieve the right account and mark the account as verified.
Add a field on the email-registration page, for instance just below the email-textbox. Directly after the user entered their email-address and pressed “register and send verification code” (don’t close the page), your app sends the email containing the verification code and the user can copy the verification code from the received email into that box.
If you want, you can also publish a service (either a rest-service, or using the deeplink) that accepts the verificationcode and validates the email-address, but it has (minor) security-issues and it adds a bit of avoidable complexity and emails are more likely to end up in spam when they contain a clickable link.