What they do to find the total amount of matter that should be in the universe is, measure the types and densities of the matter that we have found, and then use this data to extrapolate how much matter should be in surrounding space. Other factors that play a role in this line of reasoning: we know that the universe is expanding. Based on the number of galaxies and other bodies that we can see, and based on the speed at which they are moving away from eachother, we can deduce how many such bodies are likely to be found in different parts of the universe. Then, based on the matter-types we have found in observable space, we assign percentages to the amount of the total matter each comprises. Thus, based on what we know of the universe, we are able to extrapolate the percentages of matter found in the universe. Of course, there are yet more factors, such as gravity and dark matter, that have also come into play, and thus, with a great deal of effort (not so great for people using computers) we are able to make a reasonable guess as to what is found where in the universe.