Figuring out the subway is complicated especially if it's a weekend (the weekends are when the MTA does construction and even ordinary commuters find it hard to keep up with service changes). To understand the subway, you first must understand that not all trains stop at all stations. Express trains are an amazing and unique part of the NYC subway but not all run in both directions at the same time. In Manhattan most express trains run in both directions at all times but in the boroughs many express trains use a third track for one-way peak hour service. This is a pretty decent map for understanding the city. Also be aware that services are much different at late nights, see if you can get a late night map for services after midnight.