We have been investigating a microfluidics platform for high-speed, low-cost sequencing of single DNA molecules using novel "charge-switch" nucleotides. A significant challenge is the design of a flowcell suitable for manipulating bead-DNA complexes and sorting labeled polyphosphate molecules by charge. The flowcell is part of a single-molecule detection instrument, creating fluorescence images from labeled polyphosphates. These images would ultimately be analyzed by signal processing algorithms to identify specific nucleotides in a DNA sequence. Here we describe requirements of the fluidics system for loading, identifying, tracking, and positioning beads. By dynamically modulating pressure gradients in the plenum chambers of a multi-channel network, we could guide individual beads with high precision to any desired coordinate and reversibly trap them in stepped channels. We show that DNA immobilized on pressure-trapped beads can be physically extended into a downstream channel under electric force for analysis. Custom dynamic algorithms for automated bead control are described.