A two-fluid model for canonical helicity transport between merging flux-ropes is developed. Relative canonical helicity is defined here as the gauge invariant helicity of the canonical momentum of a given species, and represents the generalization of helicity to magnetized plasmas with non-negligible momentum. The model provides the conditions for when the transport of canonical helicity during merging manifests itself as magnetic helicity transfer or as generation of strong helical plasma flows. The model is applied to compact torus merging but is also relevant to situations where magnetic flux-ropes and flow vorticity flux-ropes interact. Geometrical interpretations are given.