But to actually answer your question.....for any given track in iTunes, right click and 'get info' - you can set custom EQ for that track there (you knew that bit, presumably).
However, the EQ on the iPod itself has to be set to something
other than 'Off' for those EQ settings to be used - for example, 'Flat' uses custom EQs for songs that have them, and no EQ for the rest - use another EQ and that will be iPod-global, apart from those tracks which have an EQ setting.
If you want to listen to a track (for which you've set a custom EQ) with an iPod EQ, start playing the track, then go to Settings on the iPod and change the EQ.
But instead it just kept on raining
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