This may be an oversimplification, but it has served me well. Any time the ball is loose behind the NZ, the related action is a loose ball play. No matter how many times it becomes loose behind the LOS, it's all part of one loose ball play. The loose ball play ends when the ball is possessed or comes dead by rule (i.e. incomplete pass, out of bounds). Anything else is a running play.
There can be multiple running plays during a down, but there can only be one loose ball play and it will ALWAYS start with the snap.
Once you have that figured out you just determine the basic spot, apply all-but-one (consider the exceptions) and penalty enforcement becomes much less complex.