Microchannels can separate analytes faster with higher resolution, higher efficiency and with lower reagent consumption than typical column techniques. Unfortunately, an impediment in the path toward fully integrated microchannel-based laboratories-on-a-chip is the integration of preseparation sample processing. In contrast, the alternative format of digital microfluidics (DMF), in which discrete droplets are manipulated on an array of electrodes, is well-suited for carrying out sequential chemical reactions such as those commonly employed in proteomic sample preparation. We recently reported a new paradigm of "hybrid microfluidics," integrating DMF with microchannels for in-line sample processing and separations. Here, we build on our initial efforts, introducing a second-generation hybrid microfluidic device architecture. In the new multilayer design, droplets are manipulated by DMF in the two-plate format, an improvement that facilitates dispensing samples from reservoirs, as well as droplet splitting and storage for subsequent analysis. To demonstrate the capabilities of the new method, we implemented an on-chip serial dilution experiment, as well as multistep enzymatic digestion. Given the myriad applications requiring preprocessing and chemical separations, the hybrid digital-channel format has the potential to become a powerful new tool for micro total analysis systems.