1) You make two and see by how much they differ after a certain time. (Further reading, see Allan variance.)
2) As with all the base units, we must 'define' the second in terms of something physical, which we can measure, so that we can use this abstract idea in the real world. This real-world embodiment is imperfect, and it is an engineering challenge to make something which better approximates the idea. For illustration, consider the kilogram, which is defined by a lump of metal in Paris. In principle, chipping a bit off this block makes everything else weigh more in terms of kilograms, but we immediate recognise this as crazy and we can imagine a better physical embodiment of the ideal kilogram (indeed, efforts are under way to do just this). So it is with the second: the caesium clock is the best we've got so far, but it's just a physical embodiment of the ideal second, and we can strive to make a more accurate (with accuracy defined as in (1) above).