Mp4 videos subtitles are not 'generally' supported for soft subtitles but many people use them with subs none the less. I tried adding an additional subtitle to an mp4 that already contained 2 and could not get MP4box to work in any way without the GUI so I resorted to my standby FFMpeg and found a method that seems to work even when converting from MKV<->MP4.

First MP4 to MP4. This has 1 video, 1 audio and 1 existing dvdsub subtitles:
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Name:	ScreenHunter_MP4.jpg
Views:	697
Size:	67.4 KB
ID:	34609Click image for larger version

Name:	ScreenHunter_setup_MP4181 Nov. 23 13.11.jpg
Views:	770
Size:	93.6 KB
ID:	34610

Resulting code
Code:
ffmpeg -i "C:\Users\Bud\Desktop\Various test Formats\[dp]Manjandani-1.mp4" -i "C:\Users\Bud\Desktop\Various test Formats\[dp]Manjandani-1.srt" -c:v:0 copy -c:a:0 copy -c:s:0 copy -c:s:1 mov_text -metadata:s:s:1 language=eng  -map 0:0 -map 0:1 -map 0:2 -map 1:0 -y "C:\Users\Bud\Desktop\Various test Formats\[dp]Manjandani-1_1.mp4"

Next MKV to MKV that has 1 video, 1 audio, and 2 ASS subtitles:
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Name:	ScreenHunter_Setup_MKV.jpg
Views:	728
Size:	91.8 KB
ID:	34611Click image for larger version

Name:	ScreenHunter_MKV.jpg
Views:	665
Size:	72.5 KB
ID:	34612

Resuklting code:
Code:
ffmpeg -i "C:\Users\Bud\Desktop\Iron Man.mkv" -i "C:\Users\Bud\Desktop\Various test Formats\[dp]Manjandani-1.srt" -c:v:0 copy -c:a:0 copy -c:s:0 copy -c:s:1 copy -c:s:2 srt -metadata:s:s:2 language=eng  -map 0:0 -map 0:1 -map 0:2 -map 0:3 -map 1:0 -y "C:\Users\Bud\Desktop\Iron Man_3.mkv"
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Name:	ScreenHunter_181 Nov. 23 14.04.jpg
Views:	732
Size:	17.9 KB
ID:	34613

Notice the only difference is MKV allows the actual subtitle form to be used (srt, ssa, ass) but mp4 only allows mov_text. Hopefully this helps anyone who wishes to add subtitles even though MP4 they are not the best vehicles for soft subs.