Well heres how it usually works:
You have a Primary weapon and secondary weapons. Your Primary weapon is almost always your manufactured weapon (Such as unarmed Strikes, greatsword, etc.). Usually you have the highest attack bonus with your Primary weapon, and your secondaries are at -5. When full attacking, you make one attack for each weapon (Exception: Manufactured weapons get iterative attacks. If you have multiple, see Multiweapon fighting / Two-weapon Fighting), unless your primary weapon gets in the way (IE: You can not stab someone with a greatsword and claw their face off unless you have 4+ arms).