Well, I think it's pretty simple, at least from the point of view of a theorist. You can define a complete unit system by fixing some purely conventional constants which appear in the SI units, because you have to convert between man-made units that don't fit to the fundamental laws of nature. This is understandable since in Newtonian mechanics there is no fundamental constant. The first time a fundamental constant occurred in the history of physics was Maxwell electromagnetism, where the "speed of light" entered the game, which is a universal unit in dimensions of a speed. Nowadays we know it's much more fundamental than that. It's a fundamental property of spacetime as described in the general (and thus also special) theory of relativity. In the SI it's defined as an exact value which was chosen such as to make the relation between the base unit of time (second) compatible with the base unit of length (metre). However, these are conventional units, and thus you can as well set ##c=1##, which is very natural, because space and time occur in the theory of relativity in a very "symmetric" way, although there is a distinction, because you need a causality structure to do physics. That's implemented in GR by using a pseudometric with signature (1,3) (or (3,1) which is equivalent) in the description of spacetime as a pseudo-Riemannian continuum.
The next fundamental constant entering the history of physics was Planck's "quantum of action". It's also purely conventional and will probably be fixed to a certain value very soon by the international committee defining the SI. Anyway, for a theoretical physicist it's as inconvenient to keep it as it is inconvenient to keep ##c##. So we set it to 1. Now we have only one unit left. That you can choose as some length, time, or energy (momentum or mass). In high-energy particle and nuclear physics we are used to such units and usually choose GeV as units for energies, momenta, masses and fm as units for lengths and times (as well as barns for cross sections. To convert between these choicses you only need one number, namely ##\hbar c \simeq 0.197 \mathrm{GeV} \, \mathrm{fm}## and ##10\mathrm{mb}=10^{-30} \mathrm{m}^2=1 \mathrm{fm}^2##.
The SI units are even more inconvenient, because they introduce some (from the point of view of the now established laws of nature superfluous) additional base units. One is the Ampere for electric current. In natural units it's totally superfluous, and you need to remember one more conversion factor between components of the electromagnetic field defined by ##\mu_0## and ##\epsilon_0## with the constraint that ##1/(\mu_0 \epsilon_0)=c^2## (i.e., you measure parts of one and the same quantity in different units; that's a bit like in the US where you measure distances in miles and heights in feet and inches). Another unnecessary base unit is Kelvin for temperature, which needs another conversion factor (the Boltzmann constant ##k_{\text{B}}##) between units of energy and temperatures. It's pretty arbitrary using the triple point of water and thus also pretty likely to be substituted by using simply a definition of ##k_{\text{B}}## as with the speed of light ##c##.
Anyway, in Planck units all quantities are expressed in terms of dimensionless numbers and in this sense it's the most natural system of units, defining all quantities in terms of fundamental universal constants (as far as we know today in terms of our most fundamental theories, which however can turn out to be wrong in future observations!).
Now in General Relativity there's one more fundamental unit, namely the universal coupling between the gravitational field (represented by the curvature tensor of spacetime) and the energy-momentum-stress tensor of matter and radiation, which conventionally is given by Newton's gravitational constant ##G##. Setting also this constant to 0, we are done in the sense that this also fixes the remaining freedom of the choice in the system of natural units described before. Now all quantities are given by dimensionless numbers. To convert to conventional SI units, you only need in addition the corresponding length or energy scale which is Planck length or Planck mass.