As Mark stated, hijack has the ability to adjust the volume per source. There isn't currently any method of changing eq's per source.

One thing to be aware of is that FM mode (only) has a 6dB bass boost by default. Hijack also contains a switch to turn this off. It's probable that when I rework the bass/treble controls in the near future that this bass boost will go away. (Although I might find a way to keep it there...)