I recommend having fraos just record in game sound, and recording your voice and your friend recording his voice seperately. To synch the audio, just synch up the sound of a mouse click with your fist punching in game, and match that up. When you talk through Skype, it degrades the quality of the audio a bit, so its best to have your friend record his voice seprately as well. I hope this helps.
Okay! Fraps can record in game sound, that's all. It can record you and your friend's voice but the quality is meh.
Download Audacity for commentating alone.
Download Ifree Skype recorder for Skype recording.
They're both free and easy to use and your sound quality will be great!