There is a supporting vendor on here called S.O.S. that does programming of the various modules and can reprogram the ECU for a new key when you lose both the keys.
http://www.smartcarofamerica.com/forums/f12/keys-smart-sos-diagnostics-35370/
I have not used them myself but they seem pretty reputable and have locations in different areas
Keep in mind that you have a 3 cylinder car with a MANUAL TRANSMISSION (and an automated shifting program) it is set up for economy There are a few kits to change the shifting and they will give you a little quicker takeoff, smoother shifts, etc. Both of the cruise controls have a pedal remapping circuitry that can be fun to play with, as does the GoPedal which is a stand alone unit. They won't change the top speed of the car, but will get you there a touch quicker. I use the pedal mapping on the AreA451 Cruise control on my cars (which I don't believe is available any more). The MDI cruise, which is still available also works well.