You qual as part of your pre-deployment workup schedule. You don't get issued a side arm. The AOs/AWs keep them locked up and you check them out before each flight (or it may be part of your gear...not sure what happens on the carrier now). You can have your own sidearm as part of your gear, but it's kind of a pain in the ass and (legally) it has to be a 9mm. If it isn't, the issue of where the ammo comes from will be a problem (again, legally). I'm sure there's stories of those that have got around this, I'm just sayin' what supposed to happen.
If you dig around on the site, you'll see several previous threads that cover this.