Audio and Screen Recordings do not sync up?

Hey guys, a little while ago I decided to start doing YouTube videos using Mac QuickTime to record. I downloaded SoundFlower to allow me to record system sound with screen recorder. This also means though that I have to use audio recording to record my voice. Anyway, after I started recording I had alot of trouble editing with IMovie, the two sounds never seemed to line up. One day during my recording, I looked at the times on the two recordings after I finished them. The screen recording read 25:28, but the audio recording read 25:56! They were both started and ended at the same exact time. So, my question is, how do I get the system audio and the voice audio synced up, and is there any way to get them synced in the first place?

Thanks for any help you can give me!

-Cheers! 😀