Technicalities!!! Resistances?

So, I've been trying to work out damage builds for certain AP champs, and I ran into a problem! I don't know the order in which penetration applies!

So, what I want to know is, what is the order in which these are applied?

% penetration (Void Staff)

Flat penetration (Eyes of Pain)

Resistance Reduction (Abyssal Scepter)

Also, what I want to know is if someone can have a negative resistance, and if so, from what, and what a negative resistance effect is... The reason I'd like to know is that I am trying to gauge the pros and cons of a straight up penetration build on all enemies and not just somebody running MR. what I do understand though, is that because of the exponential nature of resistances, somebody without a lot of resistances would be far more adversely effected by resistances.