When you say 'the alarm', do you mean the Toyota factory-installed alarm system (stock on the high-end option package,) or a third-party one (possibly still added by the dealer?)
If it's the Toyota stock one, then it should work seamlessly. You shouldn't even notice the alarm in your day-to-day use. It should deactivate any time you use a legitimate means to unlock any of the doors. If this is the case, then your alarm is malfunctioning.
If it's a third-party made alarm, then I have no idea. I'd check with the alarm manufacturer.