There's no problem adding pectin later in the process, you just have to be careful how you do it depending on the form. Powdered pectin can glob up if you just pour it in, mixing it with a bit of water or cooled marmalade from your pot will prevent this. Pectin sugar or liquid pectin mixes can be added without any issues.
The thing is you shouldn't need to add pectin as seville oranges are naturally very high in pectin, if you aren't getting a set then it's likely a problem in your technique or not enough sugar or acid. This very good article on marmalade has some good suggestions:
- Soak the cut peel for 24 hours to release the pectin
- When cooking keep the temperature below 220F/105C to avoid overcooking the pectin and damaging it
- Keep the cooking time short to avoid damaging the pectin
Also, make sure you have enough acidity and sugar, you generally have to add some lemon juice to marmalade as there isn't enough in the oranges naturally. If you have overcooked the pectin you can add some in, just remember to keep the temperature down and not cook it to long. As soon as you get a decent set get it off the heat.