It depends on the game. Gyruss stencils for example are all one piece and you tape off the colors you aren't painting. However, most stencils are setup as one sheet per color.
If you used the StarGate stencils, you would paint the cab red, apply the black stencil and paint. Then apply the yellow stencil and paint. The stencil guide I linked to above will walk you through the whole process.
EDIT: The stencils will come rolled in a tube. Each color is a full sheet. Check out my Robotron and Pac-man restores for examples.