Make your strokes using the pen tool directly as a Shape Layer instead of the way you're doing it.
You will see an option for line caps and line joins. They can be round or square:

To reveal the logo, put your original logo on the layer beneath the Shape Layer, then set the Track Matte on the original logo to Alpha Matte. It will use the alpha of the layer above. You may need to press the "Toggle Switches/Masks" button to reveal the Track Matte options on the layer:
Do the reveal animation by adding a Trim Path to your Shape Layer:
