Cover/Toughness are keywords that allow units to ignore X hits before any figures are removed from the target unit. Toughness is provided by units while Cover is provided by terrain.
For example, a unit in a hex with Cover 1 does not take the first hit every time one or more hits are rolled against it. Should that unit also have Toughness 1, it would ignore a total of two hits before any damage is taken.
Cover X allows a Unit to ignore X number of hits per combat roll against it. If the Unit in a hex that grants Cover X has an Engagement Token in its hex showing its own primary House symbol, then it no longer has Cover X. This is to represent that the Unit has come out from Cover to melee attack another Unit and therefore no longer benefits from the Cover. Toughness X and Cover X are cumulative, so a Unit with both Cover 1 and Toughness 1 ignores two hits per combat roll.
Toughness X allows a Unit to ignore X number of hits per combat roll against it. A Commander with this Ability applies it to the entire Unit, meaning that at least two hits per combat roll have to occur before the Unit removes a single figure. If a hit has already been ignored by a Unit with Toughness 1 that then takes additional hits from being unable to retreat, Toughness 1 does not trigger again. Cover X and Toughness X are cumulative, so a Unit with both Toughness 1 and Cover 1 ignores two hits per combat roll against it.