First, make sure you're using Knossos 0.14.0
In the general Knossos options menu (reachable through the gear icon in the top toolbar), set "Preferred Engine Stability" to "Nightly" and "Show Engine Builds in Mod List" to true. Then update the SCP mod to get the current builds.
In the mod options menu shown above, use the "Browse" button to select the most recent nightly. It should be found under <Knossos directory>\bin\FSO-20.1.0-<date>\windows\x86. The run in window options should now be in the gameplay section.