Yes, you can manually fire the controller while a script is running; however, the channel will change to whatever channel is firing in the script. Due to this, we recommend using the Manual Fire feature on the COBRA Control Panel application to more easily allow manual firing. The Manual Fire feature also displays information about the previous and next script event, including time and description.
We also suggest using the Alternate firing feature. Alternates allow you to create up to two lists of alternate events that you can fire at any time during your show.
Firmware version 4.0 introduced alternate functionality that allows you to manually fire an alternate cue while a script is running. See What is an alternate firing event, and how do I use it within my script? for more information.