Hy,
the setup of E-Mail template is in Organization Administration, correct.
You can only assigne E-Mail templates for either Amendments change (which is also a Case process) or the Cancelation of the RfQ. The templates can be assigned in the parameters as I wrote before.
There is no design to use E-Mail templates automatically for "Send" Process, this would require a customization.
If you send out the RfQ as E-Mail with print management the RfQ will be attached in the file format you selected. Furthermore the Setup of E-Mail parameters has to be done before.