In my past experiences with SA upgrades, these certificates were very similar to using your miles to upgrade - i.e. you can upgrade at any time, as long as there's upgrade space available. You can check that availability at several sites mentioned here on FT, or easieast just to call CO and tell them you'd like to see if you can upgrade such and such flight. Just mention that you already have an upgrade certificate, so you are NOT using your miles. In all likelihood, the airport will neglect to take and you can use it on your return.
If your cert specifically says it can only be used on day of travel, show up early.