[albee1952]

1. Midi Input Devices - Seems to show the connected midi devices that ProTools recognizes Just a way to enable or disable connected midi devices( rarely even look at it)

2. Midi Studio Setup - Seems to allow you to create a Midi device, but I don't understand what function this serves when "Midi Input Devices" is where you have your midi devices. And what are the send and receive channels for? This is where you setup midi controllers for playing/recording midi information to "play" Virtual Instruments. You have multiple midi channels so you can have multiple midi instruments(like MiniGrand, EZdrummer, Kontact, Ivory, etc) where each VI(Virtual Instrument) can operate on its own midi channel.(Imagine the mess of sound if holding a chord on a midi keyboard made every instrument plugin play sounds all at once). Midi channels are available both for recording midi info(notes, sustain, pitch, etc) as well as multiple channels going out to different VI's or external hardware synths.
3. "Midi Controllers" under "Peripherals" - This also seems redundant in the same way as "Midi Studio Setup". I don't understand how this differs from your plain menu of midi input devices or why it is useful.This is where you would setup a midi controller that can also control Pro Tools(like a keyboard with PLAY, STOP, RECORD buttons).

So, what exactly are you wanting to do, and what midi device(controller) do you have?