Just create a new BufferedImage with transparency, then paint the other two images (with full or semi-transparency) on it.
This is how it will look like:
Sample code (images are called 'image.png' and 'overlay.png'):
File path = ... // base path of the images
// load source images
BufferedImage image = ImageIO.read(new File(path, "image.png"));
BufferedImage overlay = ImageIO.read(new File(path, "overlay.png"));
// create the new image, canvas size is the max. of both image sizes
int w = Math.max(image.getWidth(), overlay.getWidth());
int h = Math.max(image.getHeight(), overlay.getHeight());
BufferedImage combined = new BufferedImage(w, h, BufferedImage.TYPE_INT_ARGB);
// paint both images, preserving the alpha channels
Graphics g = combined.getGraphics();
g.drawImage(image, 0, 0, null);
g.drawImage(overlay, 0, 0, null);
g.dispose();
// Save as new image
ImageIO.write(combined, "PNG", new File(path, "combined.png"));
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