The overall volume is the Master Volume control. This is controlled by the "big knob" when the LEDs are red (the default state). All of the other volumes happen before this one and it's ultimately how you control the output level while keeping everything relatively balanced by using all of the other controls. This is a global control.
The Guitar Volume happens just before the master and is how you balance the guitar level against the Bluetooth streaming audio that is coming into the unit. This is also a global control and is accessed by pressing the big knob until the LEDs are white.
The Channel Volume is like a Master for just the amp, and it is stored with the patch. It adjusts the output level without affecting the tone (like the Gain control on the amps would). This is the control you use to level your presets relative to each other. The slightly quirky thing here is that it does live in the amp processing slot, so it happens in the signal chain before the post effects. In v1.1 firmware and later, pressing the big knob until the LEDs are pink acts as a short cut to accessing this control without the app.
The Gain on the amp panel is the per-patch parameter that affects the tone of the amp â€“ also referred to as Drive
The Volume Pedal is an additional real-time control whose value is not saved with the patch. You can see in the app where it lives in the signal path.
The Master control on HD amps is considered a deep edit parameter (like sag, hum, etc.) that is saved with the patch and is exclusive to HD amps. It's the output level of the preamp to the power amp. When you load one of these models, the stored value is right for that amp in the default state and it's usually best to leave it where it is unless you are going for a very specific effect.