At least as things stand now, these signals are only used when absolutely necessary, and no real work is done on them directly. Transmitting many bits in parallel was the original way of doing this, and would still be preferred if feasible, but timing issues arise at modern speeds over long distances (10s of cm). So the signals on one board, which are still binary and parallel, are multiplexed into a multi-level serial signal before transmission, transmitted over the serial data lines, and then received and demultiplexed on the other board from multi-level serial back into binary parallel signals. All computation (logic and arithmetic) operates on the binary signals, not the multi-level signals.
