Proficiency is a checkbox. Skill Exp is spent only on that specific skill: every 10 Exp counts as 1 improvement point toward that skill. Advantage adds the selected Adv/Dis die; Disadvantage subtracts the selected Adv/Dis die. Skill checks use 1d20.
Use these rows for any weapon, armour, cyberware, feat, consumable, or mod that grants a numerical flat bonus. Enable the row, choose a target, and enter the amount. For players, armour Defence fields are summed into Damage Negation.