Not sure about the GW mod, but in the stock game, you have to be in a certain zone (roughly perpendiculoar to the target, and around 1000m or less away), then, provided you have the right ship open in the recognition manual, you get the zones, and clicking on one will let you target that zone.
Alternatively, there are copies of some of them in the wiki pages on SHIII.
http://www.communitymanuals.com/shii...hip_Weak_Spots