FFMPEG/X264 how to use them together

Question

Hey Guys

Need a little help. I am trying to encode large videos using ffmpeg/x264. While x264 is totally unable to encode these videos to .mov, ffmpeg does a decent job.

But I need to use one of the flags which x264 provides to encode my video. So is there a good way to encode large videos using x264 given that i only want .mov as output.

While using x264 I am only mentioning input and output flags, I think that may be causing the problem.

Please guide