To link emails to deals on the web application,

1. Go to Profile icon > Settings.
2. Under the Email Settings tab, enable the option Link emails to deal.
3. Click Save

The above configuration is a global setting. In order to associate an email when it is sent or received to all open deals of the email recipients, users can enable this checkbox. 

If you don't want a particular mail (like a confidential price quote) that you are sending to be listed under a deal's 'Recent conversations' section, go to the bottom of your email compose overlay, and click the three dots icon to disable the checkbox Link conversation to Deal.

Note: The global setting is the default setting and is reflected in the checkbox of the email compose overlay too.
You can enable or disable this as per your requirement.

You can view the conversations related to a deal in the Recent Conversations section in the details page of a deal.

Note: The above mentioned setting is user-specific. Each user would have to individually enable this under their profile settings.