Hey Jason, first, take a pencil and lightly shade the parts of the pattern that will be cut out. Doing this before you cut will help you keep track of the waste.
As a scroll saw instructor, I teach my students to pick a side of the blade that will be the waste. For me, the waste is always on the right side of the blade. By doing this, you will always know which side of the line is waste and which side is the project.