Well as I understand it iPods don't support ttext subs, so you would need to hard encode the subs into the video. How you would do that depends on how you were planning on converting to mp4.
this may be in the wrong forum but all i want to know is how i can merge my AVI and srt together into another AVI file. I can then convert the AVI file to Mp4 for ipod easy
As I said, that depends on how you were planning on converting. If the app supports AVISynth scripts as input, you can create an AVISynth script, with the subs and just encode that.