I recently studied Zaitsev's and Hoffman's rules for deciding which product is formed via elimination and noticed that the rules for formulated much before the discovery of electrons and any conceivable atomic theory. So how did they work out such rules without even knowing how these compounds bond and behave at microscopic levels.
This excerpt is from an article in J Chem Ed (J. Chem. Educ., 1961, 38 (6), p 297 DOI: 10.1021/ed038p297) describing the contents of Markovnikov's 1870 paper in Liebig’s Annalen (translated into English, I guess):
So this was before the discovery of the electron, but as you can see from the diagrams, the concept of chemical structure, atoms and valence was already in place.