Your only realistic option is to get on the train at Napoli Centrale, even if you've bought a ticket starting at Afragola. It's the same price either way.
So the question really is whether there is enough time to get to Napoli Centrale from Molo Beverello if you arrive at 12:20 and need to be there by 13:22. The answer is yes, there is plenty of time.
You could take a taxi for the fixed fare of €13, a bus (#151) for €1,10, an express bus (Alibus) for €5, or the metro (line #1) for €1,10.
Thanks our tickets are definantly departing Afragola to Rome Termini at 13.40pm. Is there many taxis at the Port? I think we should be ok, but I don’t know how the distance tfe I’m the port to the station and was concerned about timing!
By taxi there is no fixed fare to Afragola so you'd have to pay the meter rate. The best case in the middle of the day is probably about 40 minutes (14 miles but through heavy city traffic).Edited: 15 May 2018, 21:35
There are no normal bus services heading towards Positano at Afragola, and rather than a taxi you should pre-book a car service to Positano to meet your train.
Italo has its own special buses twice a day from Napoli Afragola to Sorrento. But these can only be booked simultaneously with a train from elsewhere, e.g. from Roma Termini. They cannot be purchased alone from Afragola.
I just took a quick look through the quadri orario on line and it looks like every Italo train coming from Termini that stops at Afragola next stops at Napoli Centrale. Some go on to Salerno and some end at Napoli Centrale.
I would get to Termini early on your travel day (or a day or two before if you're in Rome and have the time) and go to the Italo ticket office to see if you can have it changed to the Napoli Centrale. Plead ignorance, throw yourself on their mercy, the Italo employees may be more sympathetic than the folks at Trenitalia.
Even if they charge you a change fee it will be cheaper than paying for a car service all the way from Afragola. Unless, of course you're planning to use a car service from either station. In that case Afragola won't cost you that much more.
It's actually easier to go to Salerno rather than Naples because from Salerno you can get a ferry right to Positano, faster and less expensive than public transit options from Naples to Positano. Therefore, if they're going to make you buy an entirely new ticket I'd just go to Salerno.Edited: 02 September 2018, 21:21