If you create emails from a correspondence in the CRM, they are automatically checked in to the database.
This is different if you have created, sent or received emails directly using your email program. Then, the mail needs to be synchronized, i.e., checked in.
Of course, you can create emails without using JustRelate CRM, but take into consideration that a CRM system lives from the history of data and information. This is why it is required to manually synchronize all emails that are important to cases or contacts.
Emails that you receive can be stored in the CRM as email of the sender through Synchronization. You can find them as "incoming email" in the Activities tab of the external person (sender).