I've been trying to mask a shape layer with the pen tool and even though I have the layer selected I still end up with a second shape layer. Attached is a picture showing the two shape layers and no masks.
If a shape layer is selected the parametric and pen tool defaults is to create a shape. You can change the options here:
This information is pretty hidden in the user guide but it is in there. Hovering over the icons with tooltips turned on will give you the info you need. There are several tutorials on masking and shape layers accessible directly from AE's Search Help field in the top right corner of the app.
AE's interface is pretty complex and just poking around then asking questions is a pretty slow way to learn your way around.
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