Setting up the AGC properly by yourself requires very in-depth knowledge of audio processing.
If you had that kind of knowledge, you wouldn't be here asking about how to improve the audio quality, I guess.
Therefore these are the other options for using the AGC. *YMMV*
You can try some presets that are found around the internet, for example the crazy ivan preset: http://www.braingell.com/djtools/SoftSetup-SAM.htm
In any case: Only apply the AGC to the mixer, not the individual decks unless you have a very good reason to (i.e. you might want to use a different preset on the Aux decks when you're only playing one style of liners on each)
Here's another collection of random AGC presets, feel free to try them out: http://www.nextcloud.ymoq.de/s/CNJBBWFdBNbPcoz
About StereoTool: Unless you run an FM station and need to process your signal for distribution via airwaves, the basic package for 35 EUR + VAT should get you pretty far.
And about question #3: yes, I did, but I had the amazing help of an audio engineer configuring all the things for me.