As far as the Popping you referred to, you have to turn gear on and off in the right order.
From:
https://www.behindthemixer.com/pow-pop-powering-equipment-on-and-off-in-the-right-order/
Turn it on
Outboard effects and anything else leading into the mixer.
The Mixer
DSP units. These include limiters, house EQ, etc.
Amplifiers or powered speakers.
Turn it off
Amplifiers or powered speakers. WAIT! Before kicking off everything else, wait a few moments. Amplifiers store energy and need to discharge this energy.
DSP units. These include limiters, house EQ, etc.
The Mixer
Outboard effects and anything else leading into the mixer.
I would always turn the speakers on last (with volumes of other gear turned down), and off first.
As far as the loud noises when switching scenes, I don't know what is going on there. You might want to post a preset so others can help troubleshoot it. I will say that depending what is being switched in or out, there can be some extraneous sounds when switching scenes, but that is highly dependent on what's being switched.