There are a few different types of Pro Tools system, the main differences are outlined below:
Pro Tools (non-HD) with Red (Thunderbolt mode)
A new update to Pro Tools allows up to 64 inputs and outputs to be used with non-HD systems. You will be able to use all inputs on the Red Range units.
Pro Tools HD Native (Pro Tools mode)
Pro Tools HD Native systems include a Thunderbolt interface/PCIe card with DigiLink connectors. With the Red in Pro Tools mode and connected to this type of system 32 inputs/outputs will be available per Mini DigiLink connector used, for a total of 64 I/O.*
You may need an Avid DigiLink I/O License to use a Red interface in this way.
Pro Tools HD/HDX (Pro Tools mode)
The Red will connect to this sort of system in the same way as with an HD Native system, using the Mini DigiLink connectors. Please note that if you're connecting to a legacy piece of hardware that has full size 'DigiLink' connectors rather than 'Mini DigiLink' connectors that you'll need the appropriate 'Mini DigiLink to DigiLink' cables/adapters. Once again, 32 inputs/outputs will be available per Mini DigiLink connector from the rear of the Red 4Pre for a total of 64 I/O*.
You may need an Avid DigiLink I/O License to use a Red interface in this way.
*Please note that the Red 4Pre has 58 inputs and the final inputs after this number will not pass any audio.