Since HelpDesk 1.9 each Web Project can have his own SMTP connection. Web project A will receive and send emails from address A, Web project B will receive and send emails from the email address B.
You can manage all your website from one platform and with a email address for each of your project the customer will not notice that you run everything from one service.
The SMTP option from the first Web Project (ID 1) will be used for certain system emails like error messages or lost passwords, it will always be the master SMTP. However client communication is always from each individual SMTP service you setup for each Web Project.
Setup your SMTP service is the same as before.
The settings for your SMTP Mail Server can be found with your web host, if Mail() has been chosen no more information is necessary.
Another hint for Gmail accounts, activate less secure apps: https://www.google.com/settings/security/lesssecureapps and also make sure 2 step authentification is turned off.
Other services are usually much easier to setup then Google.