You can use another layer as a Track Matte. Track Mattes can use any layer's Luminance or alpha channel to create transparency.
You can also add a mask (g) to a shape layer by looking at the Tool Bar and selecting the Mask option instead of the default shape option.

For specific instructions, we need to see a screenshot of your timeline with all modified properties of the problem layers. Select the layers, press the 'u' key twice, take a screenshot, and then drag or copy and paste it to the reply field on the forum. Please don't use the "Drag & drop here or browse button files to attach" to share screenshots.