You have been using the alarm, it is passive. The system is armed when the door is locked with a remote, power door lock switch or lock cylinder.
Sorry, not sure I follow because, at least with this car (and ever since we've owned it which has been over 10 years), you had to use a specific button on the key fob to arm the TDS. If you locked it with the key or pressing the power lock button inside before shutting the door, you could pull on the door handles or shake the car all you want and it would never go off. When the alarm is active, there's a flashing light on the dash to indicate it, and that's only on when using the fob.
New remote batteries should only cost a few dollars, no programming is nessessary.
Perhaps that's for a different year or Toyota model, because according to the dealer, I would have to bring it in to have it reprogrammed (as I had replaced the battery and called them when it still didn't function even though the LED on the fob would flash when pushing the buttons as before).