Hi Ellie,
I have used Snapz for years, and I just updated one computer to Yosemite and ran into all the same problems accounted for here. There was a time when Snapz had dropped the ball in the past as well, and I switched to Voila for a bit. Worked well for awhile, and then they too had an audio issue. I just went back to it, and they've addressed it and seem much more responsive (they are already advance releasing for the next system).
I also did use that feature of recording both computer and mic sound, and needed to edit them as separate tracks. So I just went to Voila, updated to the most recent version, and did a test run. After seeing your comment, I checked that too, and ...Voila! It works!
I did a recording using both inputs, then saved it as a .mov. I then opened it in QuickTime 7 (which gives more option than any version since). Using the "Show Movie Properties" screen, it showed 2 audio tracks, and I was able to mute one and sure enough, track 1 was the computer audio, and track 2 was the mic. So you should then be able to output that and edit in a video editor (I've used Adobe Premiere Elements to do this in the past).
There are many more options with Voila, and you don't have to wait for long processing times like you do with Snapz, which is very cool. About the only thing that I've found so far that isn't as flexible is the frame rate. They give you 3 options - 15, 20, and 25. Not slower, not faster. I will likely submit that as a request. You can always do an export out of QT later for slower rates and smaller vid size. But other than that, Voila seems like a good solution.
Hope that helps!
Edit...I just had a look at the newly update Voila, and it provides screen capture options starting at 10fps all the way up to 60. They're setting up for higher rez Macs and new systems. So not bad. Wish it went down to 5.