% Reduction then Flat Reduction then Flat Pentration and finally % Penetration.
So for sorc shoes you'd bring down their total MR by 20 and then reduce that value by 40%. (55% if you have the talent in offensive)
So for example lets assume annie with magic pen reds/quints with at least 9 points in offensive for the MrP bonus and sorc shoes.
If the opponent has a base MR of 30. Then your static 15 from runes adds with your 20 from the boots giving 35 flat penetration total. This would reduce your opponents MR to 0 since penetration can't go negative.
Lets say the get a BV so now they have 80 MR.
80 - 35 = 45
45*.45 = 20 MR.
20/120 = 17% Damage Reduction
So with normal talents, runes, sorc shoes, and void staff you'll be doing 83% of your total damage to someone thinking they're safe because they bought a BV.