Skype is using pulse audio, which is part of Gnome and the main place I found to configure microphones was in the standard Gnome sound control.
How can I configure the microphones from KDE?
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PulseAudio is not GNOME-specific, but if I interpret your question correctly, you're looking for KDE tools to configure PulseAudio. See the PulseAudio page on the KDE wiki and maybe also veromix-plasmoid (and probably the “Perfect setup” page in the PulseAudio wiki but it looks down to me). Judging from Fedora's PulseAudio KDE Integration efforts,
kmix should actually already do what you're looking for.