When I started working on Knossos I originally planned to support the Cockpit Mod but I never got around to it. You can still use it, it just requires a bit of fiddling:
- Go to Knossos' develop tab. Create a new mod, choose anything as the mod ID and name. Leave the other fields on their default values.
- Create a new package if Knossos hasn't already created one.
- Switch to the FSO tab, select a build and click Save.
- Switch to your package, add the mod you want to play as a dependency and click Save.
- Click the "Mod Path" link on the left side. Switch to the sub folder for your package and drop the Cockpit Mod files inside.
- Click the Play button in Knossos. (It should be above the "Mod Path" link)
- If you want to play another mod, modify the dependency on your mod, save and click play.