In Guild Wars, to cover means to stack conditions, enchantments or hexes so that when they are removed, the more desired effects remain while the less imporant ones, the so called covers, are removed. Skills used as covers are usually low cost and/or fast activating so that they can be quickly applied or re-applied.
Examples
Using Apply Poison and Crippling Shot together will result in the poisoned condition covering the crippled condition. If only a single condition is removed, the cripple will remain, which is the more desired effect.
Using Spoil Victor before Parasitic Bond will result in Parasitic Bond covering Spoil Victor. If only a single hex is removed, Spoil Victor will remain, which is the more desired effect.