The tools that are used on after effect are-
The Brush tool, the Clone Stamp tool and the Eraser tool, these are all paint tools you can use these on each layer to paint on them, with these tools you can erase/paint on the layer and change the colour and opacity of the tool you are using and the size is changeable as well.
The settings in the paint panel are opacity, this is for brush and clone tool, this will edit the amount of paint put onto the layers and for the eraser tool, opacity changes the amount of paint removed from the layer.
Another setting on the paint panel is Flow, this edits how fast the paint or clone is applied to your film and with the eraser tool how fast paint or clone is removed from the film.
The Mode setting edits the pixels in an underlying image, blended with the pixels painted on with the paint or clone brushes on the layers.
The Channels setting on the paint brush setting includes the Alpha, the stroke will effect the opacity with the grey scale, this will effect the brush stroke or clone stroke and painting the alpha channel with a pure black has the same result as using the Eraser tool.
You have brush properties like diameter, angle, roundness, hardness and spacing.
This website is and advised website on more information on what I wrote about above and much more it goes into detail on Paint tools, clone tools, eraser tools, paint strokes and much more.