I'll try my best here.
That charger is designed to charge at 4.2v. Two 4.2v batteries will be in series, this means the voltage is doubled, so they want 8.4v now. In parallel they will take the same voltage, but want more amperage. Series is + -, parallel is + +. Series, more voltage, same amperage, parallel, same voltage, more amperage. With me so far?
IF you do plan on using stacked batteries, it's best to keep them in pairs, mark them! This way they wear the same as you cycle them. Using a brand new battery with an old battery can cause a problem. The newer one wont be restricted by the crystallization that happens to batteries with normal use, limiting the current delivery. Other wise the new one will be pushing hard, the old one can't keep up, so the new one pushes even harder and "boom" can happen.
Have a read through this, it should help some, I hope.
Basic to Advanced Battery Information from Battery University