Models in or behind cover normally fight in close combat with Initiative 10. This represents the advantage of cover: their attacks include not only close fighting but also shots against the enemy as they charge in. Apart from this, cover does not affect hits or anything else in an assault. After the first round of close combat, fighting is assumed to have swept into the cover, so it gives no further advantage to models in it. Note that cover advantage applies only to models in cover that are being charged. Some units count as being in cover all the time because of psychic abilities or weird force fields - these are of no benefit if the unit charges.
Sometimes a unit will only count as being in cover if it is assaulted from a specific direction from which the cover has an effect. For example, a Space Marine squad behind some oil drums is in cover if assaulted over the oil drums but not if assaulted from the rear. If a direct line from any of the assaulting models to the closest enemy model, before assaulting troops are moved, passes through the cover then it is assumed to be enough of an obstruction to count.
Designer's note: The Cover rules are intended to make it hard to dislodge defending units without a concerted effort. Grenades can help to mitigate this as they can force the enemy under cover during the vulnerable charge. Units with special abilities which confer 'continuous cover' do not benefit from its advantages when charging as they have to move up to close quarters where their concealment is less effective.