Please read the sticky at the top of this forum. All your questions are answered there.
In short, a simple line output converter is required to hook up your subs. Buy the Audiocontrol iPod connection for your iPod. It's the best one around and doesn't cost very much. ($~75ish?)
Actually, I'm installing my D3 Tuesday and will have my Audiocontrol unit for for sale.... PM me if you're interested.