Are you starting from the Bitmaps example? There is no support for transparency in bitmaps. There’s also no support for transparency in the background layer.
You could choose a specific color or range of colors that you don’t draw to the background layer. e.g. to not draw black to the background layer, change this code:
backgroundLayer.drawPixel(x + j, y + i, pixel);
if(pixel.red != 0x00 || pixel.green != 0x00 || pixel.green != 0x00) backgroundLayer.drawPixel(x + j, y + i, pixel);
A better way to do this in the future would be to add support for transparent graphical layers to SmartMatrix, and use an image format that supports transparency (e.g. GIF). A transparent graphical layer is pretty low on my list of priorities right now, so hopefully the workaround works for you.