Right, well I'm no expert in this either, but I'll explain how I think it works.
MP3Gain does not actually alter any of the audio data stored in the MP3 file. Instead, it analyses the volume of the file (using the Replay Gain algorithm) and stores the results in tags within the file - called "metadata" because they are information about the audio data and not actually real data.
A player that is compatible with Replay Gain will read these tags and adjust the volume up or down, in order to give every file played the same perceived loundness.
Now here's where I get lost - AFAIK, the ipod (and itunes) do not support Replay Gain (they use a slightly different algorithm called Sound Check). So, in theory, you should not be hearing any difference in volume after using MP3Gain!