Pretty sure you do it just as you described (as far as I know). You record separately and sync it in your video editor. I don't know of any program Worth using that will actually record them separately.

You can use little tricks to make syncing up easier, like start your recording and say something as soon as you hit a button or see something in the game (that won't be in the final video), that way you can easily sync those 2 things up, split them off the video and now the video is perfectly synced very easily.

Wish I had better stuff to say but that's all I have... =(

try audacity its free if you want to record separately, another way is by using sound recorder that comes with windows, lol oh but not sure how to start both at the same time though

Do this.

Record gameplay and game sound using Fraps, and your mic sound using Audacity.

You can use bandicam as alternative for fraps. It automatically seperates your in-game sound and mic sounds.:)

btw, if you are using fraps and audacity to get mic and game sound then be sure to message me if you come across any issues, i've been doing the same for a while and i'd be glad to help