Site-selective assembly of 5 mu m amine-functionalized glass spheres from aqueous suspensions onto gold surfaces patterned with carboxylic acid and methyl-terminated thiols has been achieved through the introduction of a variable tilt flow cell. In situ microscope imaging has been employed to study the four phases of assembly independently, and the relative roles of electrostatic attraction and capillary emersion have been explored. In contradiction to the commonly recognized electrostatic assembly model, detailed theoretical analysis and experimental evidence are presented to support a mechanism where patterning occurs at the point of meniscus contact. Control of pattern quality is demonstrated through the comparison of results obtained from a variety of experiments, and the best conditions for the assembly of monolayer features are identified. Finally, evidence for the extension of this assembly method to the production of singlet sphere arrays is discussed.