The main function of the Golgi apparatus is to be responsible for handling the macromolecules that are required for proper cell functioning. It processes and packages these macromolecules for use within the cell or for secretion.rimarily, the Golgi apparatus modifies proteins that it receives from the rough endoplasmic reticulum, however, it also transports lipids to vital parts of the cell and creates lysosomes. As part of eukaryotic cells, the Golgi apparatus works in unison with the endomembrane system.