Wygal

I want to etch a stock number onto a stencil and then cut the stencil. I made stencil in red, stock number in blue. Then went to Configure Cut job and assigned conditions to the colours. I went into the cut window and there it asks which condition to cut. I must pick. When cutting the design it only cuts the entire design from the cut window. What can I do to get both conditions to cut as directed in the configure, red and blue, not just one entire cut from the cut window.