Keep in mind that inserts (plug-ins) in Pro Tools are post-disk/live input but pre-fader. The track fader does not affect the signal into any plug-ins inserted on that same track. This is the same for all Pro Tools inserts, not just Eleven.
The Input LED is before the Input section of the Master section, which is prior to the first input stage of each amp. This lets you determine whether you’re clipping a signal before it enters the Eleven signal chain. The Input LEDs will light red when the signal has clipped the input. (If this occurs, insert the Trim plug-in before Eleven and use its (Trim) gain control to attenuate the signal.)
Eleven actually gives you two separate input gain stages to the plug in:
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The Input knob in the Master section, which affects the signal level before entering the amplifier model.
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The gain knob(s) on each amplifier, which control the main input stage of that particular amplifier model.
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This makes the Input knob useful for increasing or decreasing gain on amps that don’t have a separate preamp.
The Noise Gate is keyed (triggered) from the input signal. The gate is applied to the output of the amp; when open it lets sound pass from the amp to the cabinet module, and when closed silences amp output to the speaker cabinet.