If all you want to do is use your top layer as a guide then the technique below may suit your needs:

1. Scan your image in colour

2. Add a "Black and White" adjustment layer and then use the adjustment sliders to get the black/white/greyscale balance that you want

3. Change the blending mode of this layer to "Multiply" and adjust the opacity as you need.  This way you can "see"  through your "template" layer as you paint on the layers below.  It also removes the need to try and select and delete the white in the top layer as white goes transparent in multiply mode. 

4. With the "Black and White" adjustment layer selected press Ctrl+Alt+G to add this as a Clipping Mask to your template image.  This confines the adjustment layers influence to just your template image.

Using the Multiply blending mode with the opacity slider may even eliminate the need to convert to greyscale all together.

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