If you have the images, you just need to make sure there's an alpha channel around them and then start compositing them.
I do this animation all the time for Good Eats and I use After Effects for the actual animation with Photoshop to cut out the images. When using Photoshop, I don't have to actually create an alpha channel, just leave a transparency around each object.
But you can do this in Motion as well.
the key to it is to use somewhat stilted keyframed movement, not overly smooth movement.