[Headhunter]

When you fight spirits with normal weapons spirits resist 10 damage, but after that say se does 12 damage. The spirit  reists 10 damage what happens to the other 2 damage. Does the spirit take the 2 damage unregistered or does it have other defences. Also for weapons with focis does the spirit take the damage unresisted. I heard that you can ignore the natural resistance if you attack with your willpower instead of your weapon skill, and can you use your willpower with guns. If there any other rules for fighting spirit.

[8-bit]

Spirit's have condition monitors, so whatever damage they didn't resist gets marked off their condition monitor.

Spirits follow the normal rules for combat, whether physical or astral. If all of the boxes on a spirit’s Condition Monitor (either of them) are filled, the spirit is painfully disrupted and is forced back to its home metaplane. Any services it still owes are lost.

Things like Weapon Foci just bypass Immunity to Normal Weapons; meaning that the spirit does not get any Armor (Hardened or otherwise) to soak damage with. They still get to use their Body to soak damage from a Weapon Focus.

Immunity to Normal Weapons: This applies to all attacks that are not magical in nature; weapon foci, spells, and adept or critter powers function normally. If the critter also has the Allergy weakness, then the Immunity does not apply against non-magical attacks made using the allergen.

No, you cannot attack with your Willpower instead of your Weapon Skill to bypass Immunity to Normal Weapons. Not sure if that was from a previous edition, but it doesn't exist in SR5.

Not sure what you mean by "any other rules for fighting spirits". If you have any specific questions, we can answer them.

[Headhunter]

Ok so they do use their body to resist damage. I wasn't sure.

[Rift_0f_Bladz]

Body is always used in damage resistance (for thing with a body rating). Spirits have a strong hate for enemy combat adepts (due to either weapon foci or killing hands) for the abilities to ignore the spirits armor completely. For guns, you have APDS right?

[Namikaze]

No, you cannot attack with your Willpower instead of your Weapon Skill to bypass Immunity to Normal Weapons. Not sure if that was from a previous edition, but it doesn't exist in SR5.

In SR4, there was an "Attack of Will" that allowed you to attack a spirit with your Willpower rating.  There is something similar in Run & Gun:

NEIJIA
Complex Action
Neijia means internal strength. It’s as close as a mundane can get to magical weaponry in fighting spirits. The technique focuses the spiritual and mental strength of the character in order to inflict damage to a Materialized spirit as an Attack of Will. It allows the character to perform a physical version of Astral Combat (p. 315, SR5) against Materialized spirits.  The style of the attack is based on Tai Chi’s soft and fluid motion and mental discipline. The character must first make a successful Touch Attack against the spirit. This can include a Grapple or Clinch, but it also counts if the character has been Engulfed. Using only Willpower vs. Willpower as an attack, the character can impose Charisma + net hits in Stun Damage that the spirit must resist. This damage is not physical, so it cannot be used to take down wards or magical barriers. The character feels drained after making this attack, resisting Stun
Damage equal to hits (not net hits) from the spirit defending against the attack. If they are a mage they resist Drain per their tradition; everyone else uses Willpower + Charisma.

[Headhunter]

Does armour piercing affect the natural immunity

[8-bit]

No, you cannot attack with your Willpower instead of your Weapon Skill to bypass Immunity to Normal Weapons. Not sure if that was from a previous edition, but it doesn't exist in SR5.

In SR4, there was an "Attack of Will" that allowed you to attack a spirit with your Willpower rating.  There is something similar in Run & Gun:

NEIJIA
Complex Action
Neijia means internal strength. It’s as close as a mundane can get to magical weaponry in fighting spirits. The technique focuses the spiritual and mental strength of the character in order to inflict damage to a Materialized spirit as an Attack of Will. It allows the character to perform a physical version of Astral Combat (p. 315, SR5) against Materialized spirits.  The style of the attack is based on Tai Chi’s soft and fluid motion and mental discipline. The character must first make a successful Touch Attack against the spirit. This can include a Grapple or Clinch, but it also counts if the character has been Engulfed. Using only Willpower vs. Willpower as an attack, the character can impose Charisma + net hits in Stun Damage that the spirit must resist. This damage is not physical, so it cannot be used to take down wards or magical barriers. The character feels drained after making this attack, resisting Stun
Damage equal to hits (not net hits) from the spirit defending against the attack. If they are a mage they resist Drain per their tradition; everyone else uses Willpower + Charisma.

Interesting, never noticed that. Thanks for pointing that out.

Does armour piercing affect the natural immunity

Yes, it does. So, if a Spirit normally would have Hardened Armor 12, and it's being attacked with an AP -4, you treat it as Hardened Armor 8. The example on page 397 of the Core Rule Book of SR5 is a nice little snippet for how Hardened Armor works.