not to burst any bubbles here, but i find it rare for people to play with the tone knob turned down to get rid of noise. with the tone knob at 10, nothing is changed. when you turn it down from there, it starts to attenuate the highs, so actually 10 is the "normal" state of the tone knob.
with the volume knob, sure many play with it lower than 10 to clean up the amp a bit, then turn it to 10 for a bit of drive.
but because you have the clicking noise in the Apollo, it's either the guitar or something in that room causing it. i bet it's the room, not the guitar. the clicking noise gets quieter when you turn down the guitar knobs only because you are taking away gain and/or frequencies away from it. i'm pretty sure you aren't directly controlling the clicking noise with those knobs.
i feel like most electric guitarists play with the volume and tone knobs at 10 and create their tones based on that. i'd hate for you to create all these patches with the tone at 3-4 etc. and later it becomes a problem. so don't go too far with the preset creation until you try the axe and your guitar in a different room/environment/power supply.
with the volume knob, sure many play with it lower than 10 to clean up the amp a bit, then turn it to 10 for a bit of drive.
but because you have the clicking noise in the Apollo, it's either the guitar or something in that room causing it. i bet it's the room, not the guitar. the clicking noise gets quieter when you turn down the guitar knobs only because you are taking away gain and/or frequencies away from it. i'm pretty sure you aren't directly controlling the clicking noise with those knobs.
i feel like most electric guitarists play with the volume and tone knobs at 10 and create their tones based on that. i'd hate for you to create all these patches with the tone at 3-4 etc. and later it becomes a problem. so don't go too far with the preset creation until you try the axe and your guitar in a different room/environment/power supply.