Liquid-core waveguide-based optofluidic devices have proven to be valuable tools for analysis of biological samples in fluid. They have enabled single bioparticle sensitivity while maintaining in-plane detection via light-induced fluorescence. The incorporation of multi-spot excitation with multimode interference (MMI) waveguides has enabled spatially and spectrally multiplexed detection of single viruses on an oxide-based optofluidic platform. Here, we introduce a new way of MMI-based multiplexing where multiple analysis channels are placed within a single multi-spot pattern. This stacked channel design enables both velocity and spectral multiplexing of single particles. The principle is demonstrated with differentiated detection of single H3N2 and H1N1 viruses on a polydimethylsiloxane platform.