Programming an automobile keyless security remote

Question

I bought a used 2005 Scion Xa with a remote in need of a battery. I replaced the battery and the remote now works, but is erratic. I need instructions on how to program it or to use it. It has two top buttons: one with lock/unlock symbol and the other with a car trunk open. Both keys open all the locks and both set the alarm. There are also two small buttons on the side. the top one gives a continuous blue light and the bottom one flashes quickly (why?). I would be grateful for any help. Thanks!