The x16 or x8 are the lanes that each slot uses. Generally you -want- at the very least x8 for each lane that will be utilizing a GPU. Most motherboards do not support three way SLI (or higher). Most motherboards will do either a single x16 lane, or two x8 lanes. Lower end boards will usually have a setup of x16, or x8/x4, which is less than ideal for a multiple GPU setup.
As it stands today, there is a very minor performance advantage to using all x16 lanes (very few motherboards support this, most, if not all, of them are for Extreme series CPUs). x8 is ideal as there is very little performance difference from an x16 lane with multiple GPUs. An x4 lane is less than ideal and will hinder your GPU's performance.
With the Maximus VI Extreme, you'll run 4way SLI at x8/x16/x8/x8, so you have nothing to worry about with the board.