Yes, you can add comment lines to your script by using the # symbol in front of the comment line on firmware 5.0 and older. To see a sample using a comment line, please the attached cobra.csv file.
Firmware version 5.1 includes native support for script comments that are then displayed in the Show Controls section of COBRA Control Panel software. For more information on how to use this feature please see How do I use the script commenting feature?