Most of these principles were formally proposed by Nicolaus Steno (Niels Steensen, Danish), in 1669, although some have an even older heritage that extends as far back as the authors of the Bible.A few principles were recognized and specified later.This orientation is not an assumption, because in virtually all situations, it is also possible to determine the original "way up" in the stratigraphic succession from "way up indicators".
The layers of rock are known as "strata", and the study of their succession is known as "stratigraphy".
Fundamental to stratigraphy are a set of simple principles, based on elementary geometry, empirical observation of the way these rocks are deposited today, and gravity.
They are applied by geologists in the same sense that a "null hypothesis" is in statistics -- not necessarily correct, just testable.
In the last 200 or more years of their application, they are valid, but geologists do not assume they are.
Despite this, the "principle of cross cutting relationships" can be used to determine the sequence of deposition, folds, and faults based on their intersections -- if folds and faults deform or cut across the sedimentary layers and surfaces, then they obviously came after deposition of the sediments.