science_rules said:
When scientists say the position of a particle or electron cannot be known at the same time as its speed, do they mean the particle's position in reference to jumping from energy levels in a single atom, the position in reference to traveling around the nucleus of an atom, or do they mean position in reference to moving from atom to atom? Or all three?
Scientists, when very careful thinking about the foundations of quantum theory, don't say that. They rather say, as the formalism of quantum theory tells them, that position and momentum cannot be determined accurately, i.e., if you prepare particles to have a very well determined momentum their position is very indetermined and vice versa. As with any continuous variable neither position nor momentum can be determined exactly, and this is not a matter of technical problems to do so but an inherent property of these observables. It's formalized in terms of the Heisenberg-Robertson uncertainty relation
$$\Delta x \Delta p \geq \frac{\hbar}{2},$$
where ##\Delta x## and ##\Delta p## are the standard deviations for the ##x## component and ##p## that of the momentum component in ##x## direction (of course it's valid for any direction) with respect to any (pure or mixed) quantum state of the particle.
A careful scientist also would never say that anything "jumps" in quantum theory. The equation of motion for the wave function, i.e., the probability amplitudes, is the Schrödinger equation, i.e., a partial differential equations and thus nothing abruptly jumps. In your example of atoms going from one to another energy state you only have a pretty rapid transition due to the interaction with some disturbance like an electromagnetic field (or a spontaneous emission process due to quantum fluctuations of the electromagnetic field, but that's more complicated since it needs quantum field theory to be correctly described).
Finally the electrons in an energy eigenstate of an atom don't move. Energy eigenstates are stationary states, i.e., the probability distribution for position, ##|\psi|^2##, is time independent and so are all expectation values of observables.