What we want to achieve
I want to have shapes or anything for that matter have a stroke but a transparent fill. In Illustrator this would be easy but it requires a little more effort in Photoshop. Here's an example:
We want the shapes to overlap with a transparent center but for them also to have a stroke.
First we draw the shape as normal. It doesn't really matter which colour you use as this will be hidden. Now in the layers palette (Window > Layers) find the layer for the shape you have drawn and right click on the layer. You will see the following flyout menu. You want "Blending Options".
This will bring up the layer style dialog box. Give the shape a stroke by checking the Stroke box at the bottom. You can define the size of the stroke, fill colour and a few other options here.
To complete the effect return to the layers menu. You will see the Fill option. Click the flyout and reduce the percentage to 0%. This makes the fill transparent giving us the effect we want to achieve.
You can use this effect with any layer so if you have created a shape with the pen tool this will also work. Now you can happily layer up your shapes with transparent fills!