Does my son know I'm using Find my iPhone when I log on? 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&nbsp;my&nbsp;iPhone extremely simple, from Firewall iP to network logging.