The bonding sites for Au-adatom-octanethiolate within the (root 3x root 3)R30 degrees structure on Au(111) have been investigated with high-resolution scanning tunneling microscopy (STM) imaging. By establishing the relationship between the lateral positions of adsorbates on the top layer of gold and those inside an etch pit, we are able to determine the adsorption configuration with a high degree of accuracy for the elusive (root 3x root 3)R30 degrees molecular layer. The boundary between adjacent SAM domains is also imaged with molecular resolution that allows the assignment of adsorption site in each domain without ambiguity. The standard (root 3x root 3)R30 degrees alkanethiol SAM on Au(111) is found to consist of domains with Au-adatom-octanethiolate occupying the fcc hollows site, alongside domains where the hcp hollow site is occupied.