Liberty desire for Personal unions only considers that country, not your other subjects (that's part of why they're great), so getting castille won't have directly affected Naples' desire. The backing of independence is the big one for liberty desire; see if you can drag that rival into a war so they stop backing your subject against you. In general, to get LD down long-term you'll want to have as large an army as you can, and the calculation considers manpower reserves as well, so taking Quantity is a decent idea; Diplomatic and Influence will help too thanks to the Dip Rep increases - each point of dip rep gives -5 LD. Mostly, just build a big army and let your manpower recover a bit. If you have prestige or MP to spare, using the actions that temporarily reduce liberty desire might be an option - get it below 50% and the backing will stop, which helps immensely, and you can integrate Naples so as to have more men and development.I'm Aragon and I have Naples under PU. When Iberian Wedding triggers I can't keep both PU (specially Castille) because liberty desire skyrockets. I'm just too weak. To add insult to injury, someone's backing their independence. What can I do?
Failing all that, just grab some large allies so you can win an independence war, then wait till Admin 10. The decision to form Spain doesn't care how much LD Castille has, and once you've formed Spain you should be big enough for Naples to stay loyal.