The MetroCard is your key to the subway. Tokens are still available but MetroCard features discounts, unlimited ride cards and free transfers to buses. After 9 PM, the subways are less crowded and thus less safe. They are within sight of the token booth clerk. Transferring trains might get a bit confusing.
Different trains arrive at the same platform.
Always look for the train number or letter when it pulls in the station. Don't be afraid to ask questions. The train conductors are in the center of the train looking out the window.