So I am making these giant(human sized) amoeba-like aliens and to have something this big it requires a skeleton to maintain shape and to support its body but also needs to be flexible so it can do as an amoeba does and change shape to move. So my question is what sorts of weight supporting structures could allow a creature to morph shape and make pseudo-pods but still hold its weight?
There are major problems for human-sized amoeboids. Firstly, the material an amoeba is made of is basically a thin gooey substance rather like snot. To scale up in size an organism that is basically a puddle of goo is itself highly problematic. Adding a skeleton isn't enough. This will give you a creature that is a skeleton covered in a snot-like goo. This would be good for a really high yuk factor.
Also, skeletons need muscles and connective tissue to support the organism and help it move. This suggests that your amoeboid will be less and less like an amoeba and more and more like conventional animal. Less of a giant single cell and more of a normal multicellular creature that might look somewhat like an amoeba. This might not be very helpful for the creature.
Also, scaling up an amoeba's outer cell wall is likely to make it too rigid to move.
However, possibly instead of a skeleton giant amoeboids might create temporary rigidified regions of their protoplasmic body to provide support and the equivalent of effectors to faciliate movement. Not exactly legs but possibly closer to the muscle masses in molluscs like snails to move around.
This process of stiffening and unstiffening parts of its protoplasm will presumably take energy. Also, it doesn't sound like an efficient way to get around.
In conclusion, this answer has considered there are a range of major problems in scaling up what is a well adapted organism on the microscopic scale to the size of human beings where it becomes highly maladapted and dysfunctional. Some tentative suggestions have been made about possible alternative structures and mechanisms to facilitate gigantic amoeboids. Making gigantic amoeboids scientifically plausible isn't going to be easy.
It sounds like you might need the bones' equivalent of lego.
Imagine (if you will) that instead of bones, the main body of the amoeba contains small cubes of bone like material. In its natural state, the body may look like chocolate chip ice cream in that regard, with the cubes floating randomly in the main body. But when a new shape needs to be formed, the cubes are reorganised and 'stacked' within the body, with new structures being formed that are maintained in their rigidity by the glutenous material around them stiffening and holding the cubes in place.
This would allow the creature to form limbs and other appendages off a main body with some rigidity around which the main form of the creature could maintain a shape.
This answer doesn't cover the issues of musculature et al which would make the bones actually useful, but assuming that the amoeba can repurpose its primary makeup into muscles, circulatory structures et al, then all you need is the strength reinforcement which this model may well provide.