It's no prob! Last December, I only had an AD700 and no knowledge of the audiophile world. Decide to upgrade, discover head-fi, spend ~$1k on equipment so far since January and I'm sitting here with an AD2000, FiiO E12, and the never ending itch for hopefully better and synergistic equipment...
Back on topic, I use an iPod classic and iPhone 4. I find that with the BH, I have no need for source EQ unless I'm at my computer where I can do more fine tuning with the Electri-Q equalizer in FooBar. Any EQ changes you make upstream will go through downstream, though.
For example, let's say your audio chain is
If you boost the treble on your iPod, the treble will still be boosted through the BH2. Even moreso with the SF switch on since it'll "stack". I'm 99% sure this applies whether you're using the headphone audio out (3.5mm output) on your portable device or if you use a Line Out Direct (LOD; in your case 30pin to 3.5mm) to input sound from your player to the BH2.