You do get both. I can't explain it too well though so, I'm going to wait until one of the higher-ups sees this and they'll hopefully explain more.

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If an enemy has 100 MR, they have 100/200 reduced damage or 50%. An enemy with 200 MR will have 200/300 reduced damage or 67%.

Your enemy champion with 63% reduced damage actually has 170 magic resist (because 170/270=63%).

That 170 magic resist will be reduced by your 49% penetration to 86.7 MR, offering 86.7/186.7=46.4% reduced damage.

Magic penetration is calculated in terms of percentage reduction, flat reduction, flat penetration, and then percentage penetration. Your runes, which provide flat penetration, apply before your Void Staff and masteries, which applies percent penetration. A build which runs full magic penetration marks will have approximately 9 magic penetration. Let's say you have 49% penetration again.

Against a target with 50 MR, you will first penetrate 9 of that MR, lowering it to 41, and then penetrate 49% more, lowering 41 to 20.91, meaning that your enemies will be treated as if they had 20.91 magic resist for your spells only.

1. Percent reduction

2. Flat reduction

3. Flat penetration

4. Percent penetration

They add but they are calculated in this sequence.

Or rather, do enemies take increased damage if a champion has magic penetration items on and they are not actively raising magic resists?

But

flat reduction can get your target to minus values for bonus damage (correct me here if i am wrong)

In your maths

If your target has 20MR and you have 20Mpen you will deal 100 damage

If your target has 0MR and you have 2834592837592875928Mpen you will deal 100 damage.

Flat: It's MR-MagicPen/(MR-MagicPen)+100, then I find a %.

%: It's like the flat, but already reduces the %, not the flat.

And

The enemy has 100 MR, so the magic dmg taken is reduced by 50%.

I have 50 MagicPen, so I can "pass" by 33% of his MR.

That means that I have 33% MagicPen? And the damage reduce will decresease to 17%?

It's better to get flat or % MagicPen?

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Also, how does magic penetration calculate with champion magic resistance? For example, if an enemy champion had 63% reduced magic damage and I have 49% penetration, does that mean their resistance only offers 14% reduction, or 32% reduction, or some other equation?