Noise gate: in the owner's manuals

Noise gate: supported by which Fractal Audio products?

Noise gate settings (preset input) can be saved as global blocks. This applies to the preset noise gate and to the Gate block.

The Input Noise Gate on the Axe-Fx II works different from the Standard/Ultra. Adjusting Threshold won't do anything if Ratio isn't adjusted as well.
The Level parameter is not related to the noise gate. It allows sending a lower or higher level into the effects grid which can be used to compensate for guitars with varying output.
You can use SCSEL (SideChain Select) to select the signal the gate is working with. If the gate is the first block in the routing there's no need to use SCSEL. But if the gate is placed after other blocks in the routing, it can be useful to use SCSEL to set an optimal source signal, such as Input 1. This is similar to the way the ISP Decimator operates. source-1 source-2
Axe-Fx II firmware 16.02: Improved Noise Gate. The noise gate now features two types: “Classic” and “Intelligent”. The Classic type is unchanged from previous firmwares and is a basic downward expander. The Intelligent type features faster and more stable gating along with a proprietary noise reduction algorithm.

For X/Y-switching in the Gate block you need the Axe-Fx II XL or FX8. Note that there's no MIDI CC available for Gate X/Y switching on the Axe-Fx II.

Presets have a noise gate at their input. It uses CPU cycles, so switch it off (turn Threshold to Off) if you have no need for it in a preset.
It's also advisable to set the correct Instr In setting. Cliff: "To get the best noise performance it is important that the Instr In trim is set correctly in the I/O->Input menu. Set this as high as possible without clipping the input." source
The separate Gate/Expander blocks are useful for additional noise control.
A different approach to keeping the noise low: try a Vol/Pan effect with its volume parameter tied to the Envelope controller. As long as you don't hit the strings, the (input) signal is off.

The Global Noisegate Offset parameter in the Global menu offsets the Noisegate threshold for all presets. This can be used to increase or decrease the threshold to compensate for varying interference levels. If the Threshold parameter in the preset is set to “Off”, the Global Offset will have no effect. The default value is 0 dB and is set to that upon System Reset.
Matt: "When I program a pro rig, we always set the noise gate at a threshold that feels best in the studio, knowing that the global NOISEGATE OFFSET which can save you in a pinch should the rig need to be used in a noisy environment. By the way, BEFORE we had this global option, we'd often opt for a much more aggressive threshold: -65 db or thereabouts!" source

FX8 and Axe-Fx II effects threads: Compression, Volume, Gate (CMP, VOL, GTE)
Noise gate in Wikipedia
http://www.prosoundweb.com/article/noise_gates_101_what_they_do_how_to_use_them_optimally
Cliff's comments:
- "I don't use the gate at all. On the Ultra I would use the gate on high gain patches but I find I don't need it now. I did some measurements and the II is at least 10 dB better SNR." source
- "The self-noise of your guitar is usually greater than the self-noise of the Axe-Fx. This noise will be amplified by the amp block. For high-gain tones it is almost always necessary to use a gate to control this noise. Adjust the noise gate in In/Gte to squelch the noise." source
- "I prefer a fast attack and slow release and a ratio around 2." source
- "For a guitar gate you typically want the attack time as short as possible and I don't think people realize this so I changed the default value." source
- "For guitar I recommend setting the Attack time very short (less than 10ms) and the Release time to 100-200ms. Ratio 2-3:1 and Threshold to taste." Source and source