Please see the following common use-case and steps to make sure all the emails get stored on Salesforce against the right record, even when using external (non Salesforce) email clients e.g., Outlook and Gmail etc.
Make sure the "From" email address (e.g., sales@yourcompany.com) is the one that is redirected into Salesforce/e2a (as well as to Outlook of the relevant Users), so the reply will go back into Salesforce/e2a. Please see the following pages for more details on how to set up a redirection rule and set up any Org Wide email address to use as "From" address:
When Users will get a reply on sales@yourcompany.com (From email address), this will redirect a copy going to Outlook as well as a copy to Salesforce to be processed by e2a (which will attach to the right record)
When Users will reply, they should set their "From" email address to be sales@yourcompany.com so that any reply comes back in the same way as above. They can also CC or BCC sales@yourcompany.com so a copy goes into Salesforce/e2a. Alternatively to CC or BCC, a rule can be set up on their mailbox (or whole email server for all mailboxes) to redirect a copy to sales@yourcompany.com when outbound email has the From address of sales@yourcompany.com.
If you have a different use-case than the one explained above and/or need help in the email set up and e2a configuration, please feel free to contact us at support@ortooapps.com.