3D situational awareness is critical for any autonomous system. However, when operating underwater, environmental conditions often dictate the use of acoustic sensors. These acoustic sensors are plagued by high noise and a lack of 3D information in sonar imagery, motivating the use of an orthogonal pair of imaging sonars to recover 3D perceptual data. Thus far, mapping systems in this area only use a subset of the available data at discrete timesteps and rely on object-level prior information in the environment to develop high-coverage 3D maps. Moreover, simple repeating objects must be present to build high-coverage maps. In this work, we propose a submap-based mapping system integrated with a simultaneous localization and mapping (SLAM) system to produce dense, 3D maps of complex unknown environments with varying densities of simple repeating objects. We compare this submapping approach to our previous works in this area, analyzing simple and highly complex environments, such as submerged aircraft. We analyze the tradeoffs between a submapping-based approach and our previous work leveraging simple repeating objects. We show where each method is well-motivated and where they fall short. Importantly, our proposed use of submapping achieves an advance in underwater situational awareness with wide aperture multi-beam imaging sonar, moving toward generalized large-scale dense 3D mapping capability for fully unknown complex environments.