It depends on your method of voting. In many places, if you vote in person, you put your ballot in the counting machine prior to leaving the polls. While this is not an option if you vote by mail (or vote on a so-called provisional ballot), many states have a way for you to follow up after the election to track your ballot to see if it was received and counted.
The truth is I would not over-worry about your ballot being counted. The overwhelming majority of ballots are properly counted. Instead, I would use the time now to double check that you are registered and that you have a plan to vote that makes sense for you and your schedule.
As for certification, I can assure you that there will be lots of groups and lawyers working to ensure every election is accurately and properly certified.