Flow-3D sediment scours model manual (Wei et al., 2014) mentioned that a sub-mesh is applied to calculate bed-load transport. Other details are not available that how this sub-mesh works between the main mesh of the domain and the mobile bed. The reference is added here.
Wei, G., Brethour, J., Grünzner, M., & Burnham, J. (2014). The sedimentation scour model in FLOW-3D. In Flow Science Rep (Issue June).
http://www.flow3d.co.kr/wp-content/uploads/FloSci-TN99_The-Sedimentation-Scour-Model.pdf