1. When you're deciding to connect power supplies to be able to utilize the power of the charger how do you know if you want to connect them in parallel or series. As I understand it, parallel would increase the amperage and series the voltage. I would think amperage would be more important because it would allow you to charge higher capacity batteries, no?
You can't get "more current" by changing the way you wire things. A given supply will be rated for a given current. People wire batteries in parallel on big copters to get more capacity for the same voltage; think of it as a bigger gas tank, not a bigger pipe.
What you are wanting to increase with a supply to a charger is POWER, which is (CURRENT x VOLTAGE). So even though there is not "more current" when you connect your supplies in series, there is more power. Think of it this way, if you have (CURRENT x VOLTAGE) with one supply, if you wire two identical supplies in series you end up with (CURRENT x VOLTAGE x 2).
It is that power that will help you charge higher capacity batteries, and/or more batteries in parallel, and/or charge faster. How much depends on current you have at your disposal given the (input power / the voltage of the batteries you are charging).
2. I'm a little confuse on what the limiting factor on how many batteries you can charge? Is it the power or current? For example the PL6. If I use only a single 12V 47A power supply it will supply the full 40A but only about half of the power capacity. Would I still be able to charge say 8 - 5000mah batteries (assuming I used a balance board)?
It is the power, which gives you the available current which will differ depending on the voltage of the batteries.
12V x 47A gives you 564W, assuming the supply is 100% efficient AND the charger takes no power to run. In reality, the supply is not 100% efficient (some is lost in the form of heat) and the charger takes some power to run. But for the sake of discussion we will use the 564W number.
A 6S battery has a voltage of 25.2V (the voltage depends on the cell count. To find the voltage of a given LiPo just multiply 4.2V x the cell count). So if we have 564W, our max current will be 564W / 25.2V or around 22A. In order to charge a 5000mAh battery at 1C (think of the C rating for charge as the "speed" of the charge) you need 5A. So you could theoretically charge 4 of these in parallel at 1C and be under your 22A budget (or 8 at 2.5A each, just means it would take twice as long to charge all 8. might as well charge 4 at a time at 1C at that point, and make sure you only ever parallel charge batteries at a similar level of discharge).
Does that make sense? You need to consider the input power, without thinking about input CURRENT or the max current of the charger, since those are just ratings for how much all the internal components and wiring can handle. Take the input power (max current of the power supply times the input voltage), then divide that by the battery voltage to figure out how much current you can "afford". That gives you a budget to work with to figure out how many batteries you can charge in parallel, and at what speed.