Official information about this protocol is restricted by Apple to people who have joined the MFi program. Therefore, I can't mention anything of this page which isn't public knowledge.
You can get to Apple's MFi landing page here.
iPod Accessory Protocol (iAP)
This is the protocol you can use to talk to Apple devices with.
3rd Party Libraries
Microchip provides a MFi library for handling initial communication with an iPod or iPhone, as well as a hardware wrapper, allowing firmware developers to easily utilise the iAP.