I'll echo EdC on the Blue mic recommendation. You can grab a Blue Snowball for around $40-60 and they sound great.
I usually just record everything together to avoid needing to sync later. Camtasia is a great tool for screen capture and does audio pretty well.
Whichever way you go, I'd recommend encoding in h.264 in either .mp4 or .mov. 1280x720 is a great resolution for screen cap. Keep you audio bitrate at 128kbps using AAC. You can probably get away with moving the video encode to 1000kbps... any lower and quality starts to get pretty bad at 720p. Using multi-pass encoding for lower file sizes. This should give you something well under 100Mb per video file (for a 2min video).
Hope that's helpful!
