with NewtonBodySetTransform you can reset the position of a newton entity. usually physics entities get moved by forces. sometimes it's helpful though if you can reset it to any position you want. you can't simply change entity.x/y/z then because the newton engine wouldn't know about that. so you have to use NewtonBodySetTransform.

for integrating newton with the load/save system of the engine i would cycle through the newton entities and save all important properties (velocity, mass,...) before destroying them. after loading you have to create them again and reset the saved properties.