How do/did chemists observer/infer the structure of organic molecules and reactions?
Various crystallographic techniques exist, the lab technique I have used most is x-ray crystallography

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1186895/pdf/mp53000008.pdf

Currently I specialize in computational chemistry, which can estimate (with very high accuracy) the geometry of a molecule which gives the lowest energy (aka the equilibrium geoemetry) through a process called geoemetry optimization

https://www.shodor.org/chemviz/optimization/students/background.html