Don't worry if you've sent him a pre-paid phone card, your son can use it during port calls. If he uses a domestic card on an international call, most of the pre-paid companies wont' give him minute-for-minute charges. In other words, a 300 minute card may only get him 100 minutes (or less) of talk-time.
If you don't hear from you son for a while, check the boat's website. Sometimes the ship shuts down communications for periods of time. They generally post a notice when they have shut down communication.(that means e-mail too). The website (for carriers) is usually updated on a daily basis. On occasion I've found a photo or two from my son's squadron on the site, showing a jet taking off or landing on the weekly photo gallery. It makes my day (and I choose to believe he's the guy in the cockpit).
Hang in there - first deployments are tough on everyone.