The bow squares with the 1/8-inch indentation have clips meant to be attached to the string. That is, the base of the square is placed toward the string with the string captured inside the clips, and the ruler is laid on the riser at the throat. That 1/8 inch is accounted for in the markings on the square. It's 1 7/8 inches from the base of the square to the 2-inch mark. But it's 2 inches from where the clips hold the string to the 2 inch mark. They yield an accurate measurement. But like Dave, a lot of folks like to hold the base of the square on the throat of the riser and lay the ruler on the string. Using that procedure with the type of square just described will give a brace height 1/8-inch more than actual. Regardless, it doesn't really make any difference which way you do it as long as you're consistent.
Regarding nock pliers. You might check out a few tutorials on this site, or other sites or UTube dealing with how to tie on nock points. Very easy to do, kinder to the string and much less abrasive to your glove or tab than a squeeze on metal nock. Too, a tie-on nock is easily adjustable. I've actually taken to using masking tape to tape on my nock points. I use different diameter arrows, and it takes me about two minutes to take off the old and wrap on some new masking tape to change nock point height.
Good luck.