How do scientists know the precise location, etc. of the earliest supercontinents? Or their configurations far, far into the future?
Please take a look at this website, Dr Scotese explains what methods we use to determine how the earth was in the past, and indeed, what it might do in the future. We can never be sure however. He has also posted numerous videos on You Tube.
From Dr Scotese's website :

The past positions of the continents can be determined using the
following five lines of evidence: paleomagnetism, linear magnetic
anomalies, paleobiogeography, paleoclimatology, and geologic history.
Paleomagnetism is the study of the record of the Earth's magnetic field in rocks, sediment, or archeological materials. Magnetic minerals in rocks can lock-in a record of the direction and intensity of the magnetic field when they form. This record provides information on the past behavior of Earth's magnetic field and the past location of tectonic plates. The record of geomagnetic reversals preserved in volcanic and sedimentary rock sequences (magnetostratigraphy) provides a time-scale that is used as a geochronologic tool. By measuring the remanent magnetic field often
preserved in iron-bearing rock formations, paleomagnetic analysis can
determine whether a rock was magnetized near the Pole or near the
Equator. Paleomagnetism provides direct evidence of a continent's N-S
(latitudinal) position, but does not constrain its E-W (longitudinal)
position.
Linear Magnetic Anomalies. The Earth's magnetic field has another
important property. Like the Sun's magnetic field, the Earth's
magnetic field &quot;flips&quot; or reverses polarity. Fluctuations, or
&quot;anomalies&quot;, in the intensity of the magnetic field, occur at the
boundaries between normally magnetized sea floor, and sea floor
magnetized in the &quot;reverse&quot; direction. The age of these linear
magnetic anomalies can be determined using fossil evidence and
radiometric age determinations. Because these magnetic anomalies form
at the mid-ocean ridges, they tend to be long, linear features (hence
the name &quot;linear magnetic anomalies&quot;) that are symmetrically disposed
about the ridges axes. The past positions of the continents during the
last 150 million years can be directly reconstructed by superimposing
linear magnetic anomalies of the same age.
Paleobiogeography. The past distribution of plants and animals can
give important clues concerning the latitudinal position of the
continents as well as their relative positions. Cold-water faunas can
aften be distinguished from warm-water faunas, and ancient floras both
reflect paleo-temperature and paleo-rainfall. The similarity or
dissimilarity of faunas and floras on different continents can be used
to estimate their geographic proximity. In addition, the evolutionary
history of groups of plants and animals on different continents can
reveal when these continents were connected or isolated from each
other.
Paleoclimatology. The Earth's climate is primarily a result of the
redistribution of the Sun's energy across the surface of the globe. It
is warm near the Equator and cool near the Poles. Wetness, or
rainfall, also varies systematically from the equator to the pole. It
is wet near the equator, dry in the subtropics, wet in the temperate
belts and dry near the poles. Certain kinds of rocks form under
specific climatic conditions. For example coals occur where it is wet,
bauxite occurs where it is warm and wet, evaporites and calcretes
occur where it is warm and dry, and tillites occur where it is wet and
cool. The ancient distribution of these, and other, rock types can
tell us how the global climate has changed through time and how the
continents have travelled across climatic belts.
Geologic and Tectonic History. In order to reconstruct the past
positions of the continents it is necessary to understand the
development of the plate tectonic boundaries that separate continents
and bring them back together again. Only by understanding the regional
geological and tectonic evolution of an area can you determine the
location and timing of rifting, subduction, continental collision and
other major plate tectonic events.