3 hours is normal, but you should charge it before it reaches zero. It won't actually hurt if you charge it as soon as it shuts off ("zero" is not really a flat battery; Apple leaves some reserve in the battery to prevent battery damage from fully depleting it, but if you leave it at zero for a few days it WILL shorten the battery life).
The best practice is to charge the phone overnight, every night. It's very "smart" and will stop charging at 100%, so there is no danger of overcharging if you leave it connected to power after it reaches full charge. If you enable iCloud backups it will also back up automatically every night if it is connected to power and WiFi.