"Going through" something is usually a first-time experience and "going over" something is often a repetitious activity. Please note that I used the words "usually" and "often". These phrases are sometimes used interchangeably. Someone may say, "Let's go through this plan, so we know what we are facing." They could also say, "Let's go over this plan, so we know what we are facing." In this case, they could mean the same thing. Sometimes going through something suggests a more detailed process than going over something. Literally, of course, to "go through" something means to travel in a path that takes you through the thing (ie: We had to go through the town to get where we were going.) and to go over something means just that. (ie: We had to go over the mountain to get to the other side.)