We have investigated the transport mechanism of the inks most typically used in dip-pen nanolithography by patterning both 16-mercaptohexadecanoic acid (MHDA) and 1-octadecanethiol (ODT) on the same Au{111} substrate. Several pattern geometries were used to probe ink transport from the tip to the sample during patterning of both dots (stationary tip) and lines (moving tip). When ODT was written on top of a pre-existing MHDA structure, the ODT was observed at the outsides of the MHDA structure, and the transport rate increased. In the reverse case, the MHDA was also observed on the outsides of the previously patterned ODT features; however, the transport rate was reduced. Furthermore, the shapes of pre-existing patterns of one ink were not changed by deposition of the other ink. These results highlight the important role hydrophobicity plays, both of the substrate as well as of the inks, in determining transport properties and thereby patterns produced in dip-pen nanolithography.