You can use either the large holes or the small ones; they are connected together. The two sizes are there for different types of connectors that may be used. I am guessing the sizes were picked for 4-40 screws and 2-pin headers or small Phoenix blocks.
Question 3: If I want to use an amplifier to improve its accuracy, do you have any recommended gain set ?
We actually have [a version of this board that has an on board amplifier if you need one. The gain in that is changeable and you can set it up from a gain of 2 to a gain of 22.