Answering myself, since I found the solution.
I did it by extending class org.geotools.map.DirectLayer, which provides a way to define a custom layer by extending its draw(Graphics2D, MapContent) method. Graphic elements are placed at the correct coordinates by using the worldToScreen affine transform provided by geotools. For example, to define a Point2D placed at the current position given real-world coordinates:
AffineTransform worldToScreen = viewport.getWorldToScreen();
Point2D worldPoint = new Point2D.Double(currentPosition.x, currentPosition.y);
Point2D screenPoint = worldToScreen.transform(worldPoint, null);
Once the draw() method is defined, just instantiate and add as a layer to your MapContent instance.