One difficulty in organic chemistry derives from the significant number of approximations we are forced to make. You should have learned in general chemistry, how the structure of a molecule is governed by quantum mechanics; a very complex, mathematically rigorous theory. However, you and I are often expected to draw structures or provide charges on a structure we are sketching on a piece of paper, blackboard, or computer screen. How could we expect to be anywhere close to the true nature without considering QM? Many of the approximations we make (resonance, valence bond theory, formal charge) predate QM and provide an accurate model for making predictions about structure, reactivity, and electron distributions in molecules. They’ve been tested and tested over the years. Always bear in mind that what we write on a piece of paper is only an approximation of reality. QM is also just another model and also has its limitations (also because of approximations).
"The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble." -- P.A.M. Dirac, 1929