1) One approach to create deformable objects like amoeba is to use mass/spring system. You would create few springs that would control position of mesh vertices. You could use some kind of weight system to control how much springs' ends affect each vertex (like in skeletal animation). Also, springs would be affected by some forces, like gravity. Springs math is not very complicated so calculations are not so expensive. You can use Euler's numerical integration for calculations. Take a look at Hooke's law.
This is a problem under Soft body dynamics domain so I suggest you to google about it and spring systems. There is a lot of material online.
2) I think the main job is to do geometry (shape). To make it transparent just apply some transparent material.
3) Depending on your needs, you can put anything inside that geometry. If you want inside object also to be deformable, you can create similar (by that I mean object controlled by spring system) but smaller object, or you could just render same object after applying some scaling to modelview matrix.