By default, Conga Contracts Send for Negotiation functionality will allow users to select any Salesforce Email Template in the system. However, only some templates will be useful for Send for Negotiation. For orgs with a large number of existing email templates, we recommend filtering the list down to only those in specific Email Template Folder meant to be used with Conga Contracts.
To do this, first create a new Email Template Folder for your Conga Contracts email templates, then select it from the dropdown on the setup page (which controls the global setting for your org). If more granular configuration is needed, this setting can be modified for particular user or Profiles by going to the custom setting directly.