If I use Find my iPhone to locate my son's phone, does he know I am checking? Does his phone alert him that I'm checking on him?
By default, no, there is no way for them to know the device is being viewed through Find My iPhone.
However, your son could enable System Services status bar icon so that the device shows the location services icon in the status bar when any system service location tracking is active.
- Settings → Privacy → Location Services → System Services → Status Bar Icon
This shows the normal location services icon (and not a special icon for Find My iPhone) if the device's location is being obtained through Find My iPhone.
Whether your Son has other location services that would cause the icon to already show or if he would notice the times when the server asks for an update is another story, but it's possible for him to get tipped off if he changes one setting.
Furthermore, if the device is jailbroken, there are numerous tweaks which would make detecting Find my iPhone extremely simple, from Firewall iP to network logging.
Since the question was "will he know" and not "is there any way to know", I've decided to answer:
Maybe he'll figure it out but probably not. It really depends on how much he's paying attention. @grgarside's answer is technically correct that he can turn on a setting which puts an arrow on the screen whenever the phone it figuring out it's location. But it's subtle and doesn't show on the home screen which app is determining location. Also, if you're tracking someone for an hour, it will only show the icon on their phone about once every other minute for about 5-10 seconds each time. So it's very subtle and the arrow does not stay on. There is no way for him to set the phone to alert him (set off an alarm) if he's being tracked. And even if he sees the arrow on screen he might not make the connection that she's tracking him. Because lots of other apps also use location services.
Will he know that she's tracking him? NO. The most would be that he might suspect it.