Don't get hung up on what you might have done differently before! They will be counted as three convictions, but that makes no difference to when they become spent, and once they are spent they will remain spent. You will need to make sure that you have paid the compensation to the court, though, as they will not become spent while you have an outstanding compensation order. It is worth checking with the DBS to make sure that they have the compensation recorded as being paid in full. If they haven't, then you can contact the court to ask for written confirmation that you have paid, which you can then forward to the DBS.
Regarding telling an employer about how many convictions you have, as it isn't exactly obvious what is going on, you can just say that it looks like they are listed as two convictions, so that is what you told them.