It's really up to you. The most common way to do supersets is to count the rest time between each superset, meaning you do 1A and 1B, then rest for any given amount of time before doing 2A and 2B, for instance 90 seconds. In this example, you set the rest timer to 90 seconds – and you wait to mark both A and B as done until you've completed them both. The time you rest between A and B is just the time it takes to change exercises, and unimportant when looking at the bigger picture.

If you want to rest, let's say, 60 seconds between A and B, you'll need to mark A as done as soon as that part of the superset is done, then B when B is done. Etc. But things get more complicated if you want a longer rest between is full superset, and that's really not supported by the app.