From my understanding, the set bonus is based on all seconds skipped between rounds throughout the whole game, whether the set was equipped to a tower or not; and activates, and is only active, with all three pieces equipped to a tower. Every tower with the full set gets the same bonus and the set doesn't become useless once the bonus round hits, but you can no longer increase the bonus (which is usually substantial anyways.) Just fyi skipping the 30 seconds before the bonus round starts adds no more bonus to the set. It's a great set for any speed reliant tower and is only matched in speed increase by the mummy bandages on a high level tower, which is an epic item.
tch is correct. It will add all the skipped seconds even if the set is not yet completed. Also, it will transfer the bonus if you equipped it to another tower.