Attack Rolls
Bonuses and penalties apply to these rolls, just like with other types of checks. Weapons with the tracking trait add an item bonus to your attack rolls, improving your ability to hit targets.
Melee attack roll result = d20 roll + Strength modifier (or optionally Dexterity modifier for a finesse weapon) + proficiency bonus + other bonuses + penalties
Ranged attack roll result = d20 roll + Dexterity modifier + proficiency bonus + other bonuses + penalties
Multiple Attack Penalty
The multiple attack penalty doesn't apply to attacks you make when it isn't your turn (such as attacks made as part of a reaction). You can use a weapon with the agile trait to reduce your multiple attack penalty.