Harmony has two ways of adding transparency to your scene:
The Opacity parameter is a parameter each drawing layer. It is set to 100% by default. By lowering it, you can make an individual layer appear more transparent.
The Transparency effect is an effect node that can be attached to individual layers or to a composite. It has a Transparency parameter that is set to 50 by default. The higher it is, the more transparent the layer or composite it is attached to will appear.
It is important to know when to use either approach. For example, to make a character composed of several layers transparent, it is preferable to connect the character rig's nodes to a composite and connect the Transparency effect to this composite, as reducing the opacity of individual layers will make their overlapping parts visible—see About Composite Nodes.
You can however animate a Transparency effect's parameter in the Timeline view, so this may be a preferable approach even if you only want to animate the transparency for a single layer. To learn how to add and animate an effect, see Adding Effects Nodes, Connecting Effects and Animating an Effect.