There are 4 general contributors to the mass density of our co-moving patch of what may be a larger universe:
(1) Visible baryonic matter (including clouds of baryonic matter which may be visible only as shadows blocking galaxies). NASA estimates 4.6% of all matter is baryonic (http://map.gsfc.nasa.gov/universe/uni_matter.html).
(2) Dark matter (not visible, but gravitationally interacting with itself and with baryonic matter). Dark matter is about 24% of the mass of the Universe, according to NASA.
(3) Relativistic particles (photons and neutrinos). These are a negligible part of the total current mass of the universe, but they provided a much larger contribution in the early stages of the Universe.
(4) Dark energy - about 71.4% of the mass, according to NASA.
If our Universe (or at least our co-moving patch) is flat, all these contributions should sum to a density just sufficient to allow the Universe to stop its expansion after an infinite time without collapsing into itself. This critical density may be considered a boundary which is less than a density which would cause the Universe to curve back into itself (closed universe), and more than a density which would allow the Universe to curve away from itself (open universe).
This critical density is sometimes represented as a ratio of 1. Here is a link to an accounting of contributions to total density of the Universe: http://hyperphysics.phy-astr.gsu.edu/hbase/astro/denpar.html. You'll notice, however, that the linked page differs from NASA's estimate. It claims 27% baryonic and dark matter, 73% dark energy; and its estimated split between baryonic and dark matter is not in synch with current consensus science, as Ross Millikan points out in his comment below. Nevertheless, I've linked to this GSU page because its method of accounting expresses the critical density of the Universe as 1, and all the contributions as a fraction of 1. The GSU estimate actually adds up to something slightly greater than 1, which is problematic as it would indicate a closed Universe.
The problem with a density that departs from the critical density is that inflation, the theory that explains the large scale homogeneity of our Universe, requires our Universe to be flat.
One estimate of critical density has it to be about 9.47 * 10^-27 Kg/m^3. But we are aware only of our co-moving patch in what may be a larger Universe. According to Wikipedia (https://en.wikipedia.org/wiki/Observable_universe) the volume of our co-moving patch is about 4 * 10^80 m^3. That estimate should include volume that is not visible but which in theory could have existed before the Universe became transparent. Density requires mass as well as volume, and this link is to an example of how one researcher estimated the mass of the Universe: http://www.scientificjournals.org/journals2009/articles/1437.pdf.
Fluctuations in the energy density of the early Universe may have become the large scale structure we now observe. The tendency of galaxies to cluster and to follow filaments of dark matter, can provide clues to whether our Universe is closed, flat, or open. Dark matter exerts gravitational attraction to visible matter, which appears in maps of galaxy clusters. Here is a link to a map of one small part of the universe, showing how the visible structure of the universe clusters along filaments, which are thought to be dark matter: https://en.wikipedia.org/wiki/File:2dfdtfe.gif.
Biasing of galaxy clusters along what may be a substructure of dark matter could provide evidence of how mass-energy fluctuated in the very early stages of our Universe, and how it acted during inflation. Here's a description of how to quantify biasing of galaxies and clusters as non-local phenomena, and includes a way to measure it without having to assume a pre-determined structure of dark matter: http://ned.ipac.caltech.edu/level5/March12/Coil/Coil5.html. If you navigate through the entire website, you may find it an excellent introduction to the large scale structure of the Universe, and an answer to your question of how researchers determine where visible and non-visible baryonic matter lies, and its relationship to the location of dark matter.
The dynamic process of how baryons may have precipitated from denser matter into their present configuration may be accounted for by "friction" with dark matter. Here's a link to a paper that explores this: http://arxiv.org/pdf/astro-ph/9410093.pdf.
This link is to an account of the most recent mapping of dark matter: http://www.sciencedaily.com/releases/2015/07/150702112045.htm. Here's a link to a summary of how evidence for dark matter is collected: http://www.astro.cornell.edu/academics/courses/astro201/dm_evidence.htm
In sum, yes, it is believed that visible matter and dark matter cluster together in filaments.