Found how to update Custom Fields using CommandByEmail

The correct syntax is

CustomField{CFname}:

If the mail is creating a new ticket, the Queue should be set at the top of
the email, so the Custom Field that is specific to the queue can be updated.

Thanks to Kenneth Marshall for figuring this out!

Niki Serakiotou
Client Services Manager
Rice University Division of Information Technology
cell: 713-992-1327
office: 713-348-4887
Address: Mudd 106C, Rice University, 1600 Main Street, Houston, TX 77005