Welcome to the fam my freind 
Sometimes you just have to “spell it out” 
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Not all, but most of us heavily use what we grow so we are Sometimes a little slow to the draw 
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But yes you will mix up your jacks or any other nutrient line and that goes into the reservoir.
RO water or distilled is what most use.
But i have no issues with useing my tap and/or rain water in mine.
Once you turn on the autopots, nothing goes in from the top anymore other then if you get bugs of some sort you could find yourself adding something to the top like Mosquito bits or pesticides…
But since autopots bottom feed, it pushes the salt build up to the top layers of the coco, (or whatever substrate is in the pot) .
Only time with autopots you do not add nutrients to the reservoir, is if it’s an "organic " source of nutrients or something like recharge. Something that isn’t going to flow through the lines very well.
Using recharge as an example, if i want to add some to my pots, i would take a bit of solution from my reservoir, 1 cup full per pot maybe.
Mix a little recharge in it and pour that cup straight into the tray where the float is, basically bypassing the reservoir and water lines…
and i just realized the date says March not May so you probably figured all this out by now 
but i typed this all up so only seems right to hit send 
Happy growing my freind and show us what you got going if ya want to, we like bud porn 