Update: for some reason, I thought you had a 3200. The 4800 has more 'full featured' channels - ie - those with EQ/Dynamics and Aux efx. So you can use 41-48 (which I'm not directly familiar with but assume offer the same features as those on Layers #1/2.)
The problem with bussing faders to your recording source is, everything on those channels gets printed to the tracks. If you enable the EQ, it goes along with the signal all the way to 'tape - destructively. Input Bypass does just that - it bypasses the DM altogether, patching the source input (M/Line or outboard preamp/efx chain) directly to the target recording medium. You then assign the same source input to a separate DM fader for purposes of monitoring during recording. That fader's position, nor anything else added within that module, affects nothing on the recorded signal. It can be auxed, EQ'd, and compressed while being monitored without having any bearing on the recording itself. That leaves you room to experiment with various things, all the way to the final mix, using a 'dry' signal to work with.
That way, there's zero latency because the summed combination of signals is monitored on the DM where everything arrives simultaneously without delay. If you're using ProTools 'standard' - not 'HD' with proprietary hardware - there is no means to monitor and track out of the box, while hearing the new track being recorded without a few microseconds of annoying delay. So, by splitting the signal in the DM - one side bypassed to the DAW, the other assigned to a fader for monitoring - you defeat latency altogether.
Hope that makes sense.
CaptDan