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?
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,