You can blit bitmaps over the rendered image using the blit()-methods in FrameBuffer. That's what the fps-demo does...When using the software renderer only, it's also possible to use AWT/Swing in combination with the rendered image but in respect to (possible) OpenGL support, i won't advise you to do so. If you use the blit()-methods in FrameBuffer, make sure to use the one that operates on Textures instead of int[]. It's usually much faster.
It's possible to "pick" an object with the mouse. Just add a MouseListener to your Component (our use the LWJGL was of doing it...it all depends if you decide to use OpenGL or not) and have a look at Interact2D. It offers methods for picking objects with the mouse.
Hope this helps.