All the sources that ScreenFlow records will go into the media library of the ScreenFlow document. ScreenFlow will combine certain audio sources with certain video sources. For example, webcam and microphone together or desktop and system audio together. If you want just audio you can isolate it and export it as an audio file.
Mathias I've been using Screenflow through several iterations and at no time that I remember did it record separately. Audio is recorded separately if you have a dedicated audio source. For example, when I record a typical screencast I'm capturing the screen on my computer, but I'm also capturing the audio via an independent mic/amplifier. So, in that case, the audio does come into Screenflow as separate files.
As already said, quite easy to separate out after recording if you are capturing both audio and video from the same source. Just right-click on the relevant track and an option will pop up that says something like "detach audio".