iOS devices can play back mp4 files with certain settings native, check the spec page for that and Google around a bit to learn about the amount of key frames etc.
You can just merge the srt files in to a mp4 file, there are lots of programs that can do this very easily such as mp4toolbox and Handbrake.
If your source is a mkv file then I would recommend to check out mkvtomp4, you can find it here: http://forum.doom9.org/showthread.php?t=163050