This is how I did it on a 2002 Tracker. Both remotes mysteriously quit working after coming back from the shop. I got this from the Suzuki board where they said it would only work for 2003 and up Vitaras...
If transmitter/door
lock controller is replaced with new one or additional transmitter(s) is necessary,
program transmitter code(s) as follows:
1) Confirm that all the doors are closed and the ignition key is out of the ignition cylinder.
2) Open the driver’s door. Insert the key and turn the ignition switch to ON position within 10 seconds.
3) Turn the ignition switch to OFF position within 10 seconds, remove ignition key from lock cylin-der.
4) Push and release the driver’s door switch (1) 3 times within 20 seconds.
5) Insert the ignition key and turn the ignition switch to ON position within 10 seconds.
6) Turn the ignition switch to OFF position within 10 seconds, remove ignition key from lock cylin-der.
7) Press and hold both LOCK and UNLOCK buttons (2) on the transmitter (3) for more than 5 seconds
within 20 seconds of removing the ignition key from the lock cylinder in step 6.
8) Press LOCK or UNLOCK button (2) on the transmitter (3) within 5 seconds (after step 7). All the
doors will lock/ unlock to confirm that this process has been properly done.
With this process, the transmitter has been programmed.
9) If you want to program an additional transmitter, repeat the procedure from Step 1) through Step 8).
10) Make sure that the keyless entry system properly operates by operating each transmitter.