You can reply to your domain-name email the same way you would reply to any email in your Yahoo! Mail account. Keep in mind that when you reply, your Yahoo! email address (you@yahoo.com) will appear in the "From" field — and not your domain name email address (you@yourdomain.com).
If you'd like to use your domain name email address when replying to email, you will need to upgrade your plan to either Custom Mailbox or Business Mail.