Can someone tell me how to do this?

I have a bunch of mkv files that have H.264 video but the level is at 5.1, and i want to convert them to 4.1 for playback on my ps3

Its kind of a tedious process doing it through the gui one by one, so how can i do it all at once?

Also if anyone could be so kind as to tell me what these to options mean?

Add picture timing info
Continually insert SPS/PPS

Thanks