skinning problem
 

how do i stop the skeleton deforming parts i don't want it to.

e.g. how do i stop the arm deforming the side of my model?

post pic up mate.... Is it rigid or smooth bid?

More than likely you need to distribute the weight in such a way to not deform against your wishes. Check out our rigging video tutorial series.

found my problem after going through each joint and painting my weights they hadn't been held.

if it was smooth skinning, you can also put some of the joints around like ribs. Its eazyer than repainting skin weghts sometimes..