I have some speakers connected via the headphone jack and want to control the bass etc. Currently all music is played through iTunes.
I'm not sure you're suggesting that you want to control just the EQ of your music while playing in iTunes or if you want to control the EQ of the whole system.
iTunes has an equalizer you can access via Command-2 and contains several presets. If you're looking for more bass, try the Rock preset.
If you want to control EQ for the whole system you'll have to hijack the audio. I found this post that provides some steps though I have not tried them myself.