How to get the pen tool to not draw over layers above the layer I'm drawing on

I have a layer that I handwritten in and added strokes to the text to make it pop more. What I want to do is make the text's color fuller by coloring the letters with the pen tool, but even after separating the effects into their own layers and putting it above the layer I want to color in, the pen tool still colors over the strokes. Locking the layers above does not change anything either.