So I recently purchased a 7.4v Batterypack split it in half to get two slimmer portions, but my question is are these already equip with the protection board(s) or what are those boards on top of each for?
That board makes it so you don't break the tabs off the battery when you are connecting to them. They do not have protection circuitry on them, they are simply a easier way to connect to the battery.
Got this protection board in the mail and understand the wiring diagram it gives you I believe, in order to connect to your DPDT switch and charging ports you would run your ground and power lines off of the p- and p+ on this board right?
You can desolder them if you want. I would not recommend that because the boards make it less likely that you'll break off the battery tabs, as he said.