Well what makes a system unique? The observables that help define its properties. Stuff like the system's energy, spin, momentum, position, etc all help to uniquely define the system. The system's state is defined as the combination of eigenstates, wavefunctions, of the system's Hamiltonian. This will make the expectation value of the system's energy one property that we can measure. If the system can have eigenstates that have the same energy, called degenerate states, or if we can have a different and unique set of states that can produce the same expectation value of the energy (within statistical measures) then we just need to look for more properties to uniquely define the system.
If we need to measure multiple observables, we want them to be commutable because then we no longer have any inherent restrictions on the precision of an ensemble of measurements. If we have degenerate cases, we can usually apply conditions that will raise the degeneracy, like the application of a magnetic field with Zeeman splitting. Either way, once we have determined a set of observables that will uniquely determine our sytem, all we need to do is measure our systems and pick out the ones that match. Even if a system is in a superposition of states, a measurement will cause the wavefunction to collapse on the measurement. So if I want state with energy E_1, I measure systems until I get E_1 and then that system has now collapsed from any superposition of states to that one state that is E_1. So in a way, measurement can help ensure the starting point (unless you are looking for a superposition of states as your system).
As for the second set of statements. Let's say we have a system that has a three-fold degeneracy for the second energy level with an energy eigenvalue of E_1. However, the three states here differ in terms of two uncommutable observables, let's say A and B (whatever they may be). So, uncertainty principle states that the product of the variances of A and B will have a lower limit. However, if the expectation values of A and B are sufficiently different between the three states, then it may still be possible to uniquely define the system. Our data will be scattered about when we plot it out in terms of <A> versus <B>, however, if we do it correctly the means should still be around the unique mean values. So while it we may not be able to precisely measure A and B at the same time, we may be able to measure them with enough precision that we can separate the measurements amongst the three states.
This is not exactly what I am talking about but a demonstration of the splitting none the less. Take a look at the Stark effect (
http://en.wikipedia.org/wiki/Stark_effect) or the Zeeman splitting (
http://en.wikipedia.org/wiki/Zeeman_effect). Let us say that we can only accurately and precisely measure the energy of an atom in an excited state but we wish to only have a specific spin with the electron. Normally, there are a number of degenerate states to the higher energy levels that have the same energy (from simple quantum analysis) but differ in their spins and angular momenta. However, if we apply a field, the difference in the interaction of the spins and momenta lifts the degeneracy so that the different states now have different energy levels. By increasing the field we can make the differences strong enough that we should be able to correlate measurements to the specific states.