Epithelial tissue function requires a robust, reciprocal interaction between cell-cell contacts and the apical-basal polarity axis, but the precise nature of this interplay is not well understood. Drosophila cellularization provides a superb model for examining junction formation as polarity is first established. Work from our lab and others identified Bazooka/Par3 as a key polarity cue required for adherens junction formation during cellularization. Canoe/Afadin, which links adherens junctions to the underlying actin cytoskeleton, and its regulator Rap1, act upstream of Bazooka. We recently found that Rap1 acts at multiple levels during polarity establishment, facilitating retention of Canoe at the membrane, and also directing correct apical positioning and organization of Canoe into supermolecular assemblies at tricellular junctions. We show that the Rap1 GEF Dizzy directs a subset of these events. Our data reveal that regulation of apical-basal polarity establishment by Rap1 requires a diverse set of inputs that specify unique aspects of Canoe’s behavior on the polarizing membrane. In the current model, Rap1/Canoe, Bazooka and adherens junctions initiate polarity, and subsequently other protein complexes are recruited to elaborate on the polarity program. Our latest findings indicate this linear hierarchy is significantly oversimplified. Instead, proteins of the basolateral Scribble polarity module are required at the onset of polarity establishment to spatially restrict Canoe to apical ends of polarizing cells. Strikingly, mislocalized Canoe puncta continue to colocalize with adherens junction proteins. Thus Scribble is critical for the supermolecular assembly of smaller cadherin-catenin complexes into mature spot junctions and the positioning of these junctions apically. Intriguingly, overexpressing Canoe in a scribble RNAi background altered architecture of the mislocalized Canoe puncta, with assembly of more contiguous structures that may represent enhanced clustering. These data form part of a larger scale effort in our lab to define the full network of proteins and mechanisms by which individual cadherin-catenin complexes are assembled to form apical adherens junctions, of which serve to direct elaboration of apical-basal polarity.