My understanding is that the percentage is used as a multiplier for the player's ratings to determine their "performance while injured" for a particular game.
So if a player has a Perimeter rating of 100, but is at 85 due to injury, then his perimeter rating for that game effectively is 85 (100 x .85).
At least that's how I've always handled matters when determining whether or not an injury is significant enough to warrant juggling my starting lineup/playing time in a given game.