When we are generating a new email is it best practice to start this in Outlook or FYI?

This is really up to the user's preference.

If you create an email from Outlook, unless you select these from the FYI Drawer in Outlook, it will automatically file the email with the filing defaults for that client if these have been set (refer to Setting Filing Defaults for a Client) or using your own defaults (Refer to Setting Defaults and AutoFile Defaults for your Own Login - My Settings).

However, if you create an email from FYI, you can change the filing details in the Drawer before you send it.