The GOTSent program is the easiest and most reliable one for me. Just one click, no need to do it few times.
Don't do anything to the audio section, it will automatically choose after you browse for the file, depending on your input MKV.
Except if the MKV has more than one audio stream, only then you have to select the main stream.
If you want the audio to maintain as 5.1 channel, you need to toggle on "Mux to VOB", this because the MP4 container doesn't support multi-channel audio. And in the "AC3filter Options" choose output as "3/2+SW 5.1 channels". This only if you remux to VOB with 5.1 audio. If you don't select VOB, the program will convert the audio to 2-channel AAC remux it with the video.
Remember, this remuxing process never touch your video, so the picture quality will remain the same. That's why the process is so fast.
For me it always work with 720p MKV movies, but for 1080p it mostly don't work. Which is fine because every remuxing program I know doesn't work for 1080p on PS3 either.
I hope you can get it working this time. Good luck!

hmm...no idea what happened...it just crashes after progress 100%, and also after the mkv file splitted into 2.. (few times already)...anyway, so that means that after i choose the mkv file, and the audio was set to DTS, it's ok to leave it as DTS ya? cause i heard ps3 couldnt play dts...i must split the file?