Or to put it another way, the second night of a two-night weekend stay (Fri/Sat or Sat/Sun) is free. You pay for the first night.

With this in mind, the best use of the certificate is for a weekend stay where the first night is cheaper than the second. For example, I've found the standard (rack) rate at the Yokohama IC to usually be about 40% cheaper for a Friday stay than a Saturday stay or a Sunday stay. So a Friday/Saturday two-day stay is the better deal than a Saturday/Sunday two-day stay. Reserve (only!) the Friday at the Advance Purchase rate, and you're even better off.