Whenever you email a client with a correspondence that relates to an existing CRM opportunity (i.e. an "as per our conversation" about when you think the project would get going etc.) you should track it in CRM so it is centralized and can be seen by anyone else who tries to follow up that opportunity.
The simplest way is when writing or receiving the email in Outlook, click the Dynamics 365 button and then "Track without Regarding".
Track all in a thread or just one?
Track all in a thread - except if they’re irrelevant (no useful information for anyone), but that’s quite unlikely... so basically it is “all tracked”
Note: with the old CRM COM add-in, this was automatic once you tracked the 1st email on the thread, the rest would be auto-tracked. That is no longer the case so you now have to track every email manually
Now you know the general principle, the next step is to determine what activities are worth tracking: Sales - Do you track all sales related activities in CRM?