Every Level adjustment function has its purpose. You should use it for that and not for other things.
The Word you are looking for is called “gain structure”. Just read about it, there are plenty of HowTo’s out there going into details.
In short:
Always keep signal levels as high as possible as long as possible, but never too high. Lowering your signal level means your signal has less distance to the noise floor, which at the End also results in less usable dynamic range. A too high level means overdriving and clipping which sounds terrible. You simply want as low noise as possible and absolutely no clipping (which obviously is kind of a target conflict).
The difficulcy is that you can almost never know exactly how high a signal level will rise (and start to clip). You have to guess that. So all Level Controls need to be checked often and good metering is an important Part of that checks. SQ has mighty tools for that - you should absolutely learn how to use them!
Best Practice is to leave some “headroom” of level range which ideally gets not used (but helps if you guess wrong) - how much depends on your signals and your hardware, on a SQ 12-20 dB Headroom might be a reasonable point to start since it has a really fine dynamic range and 24 Bit samples. With that you are still beyond the quality Level that an Audio CD could even deliver. Beware: the metering might have a “0dB” Mark which already gives some headroom, check your documentation for that!
Additionally it might be a good Idea to use Brickwall Limiters on (or before) Inputs. They at least can stop going into hard clipping too much. Setting them to stop Peaks at 2 to 6 dB below the Hardwares clipping point should be safe. Sp if you work correctly, they never do anything at all. If you make a mistake they can reduce damage dramatically.
The Rest is “source to drain”. Use the Gain Control to keep the Peaks of your Input Signal at the Headroom level. Use Channel Faders to adjust relating levels between Signals and keep the Mixing bus on reasonable signal levels. If there is one, use Master Trim/Master Gain to adjust the Peaks to Headroom level.
To set your overall Show Loudness, it is best to set reasonable Levels on the final Amplifiers or with large PA Systems on the System Controllers the Mixer delivers its output to.
The Master Fader should be used to fine-adjust loudness while the show is running or to lower overall Volume temporarily because the Gig needs that (for example: on a Party, you should use Master to set different Levels for Dancing and Chilling time).
If you use Groups, it is the same, you just have one more gain stage to control it is easier to make groups of Signals more or less Loud in relation to the others.
If you cannot access the frontline levels directly, it is the least bad way to use your Master Fader for that (or route Master through a Matrix which can be used to set a reasonable maximum loudness so you can put Master to around 0dB on normal (loud) Operation.