How can I programme a spare key?

Yes, you can only unlock the doors. I did the same thing with my 2000 Altima. The original has a chip in it.
A new key with the chip will be quite expensive. The cut key without the chip will turn the engine over but it will never start.
But you will at least be able to get in the car with the spare key if you accidentally lock the keys in the car.

Try and recut the key if it don't start the bike it has a chip and needs to be cut and flashed at the dealership

put blank spare in the wallet , thieves love easy to find spare keys.
i even cut the heads off keys (hacksaw) so the end part fits in my wallet. no plastic bulge. wife has purse, so can carry bricks easy.
done this for 50years of driving.
my jeep does this and is a feature, but is reset at door exit.
my jeep locks above 15mph. and is programmable.
so did you read your operators guild on this?
so RTM, first.
or reset the system.

You can buy a key programmer tool to help you , i know this website ,there are many car diagnostic tool on it ,you can choose one for your car www.drsets.com

you can use the sbb key to copy a new one, Before running SBB key programmer, please insert the blank new key into your car keyhole;turn on ignition switch;Insert SBB 16-pin interface into your car OBD2 diagnostic seat. SBB key programmer copies chip according to car model, and it program key not clone key, it only needs to insert SBB. It is easy to do, you can DIY, if you don't know about the knowledge of the car repair, you need call for help of locksmith....

is it an after market system or factory?

research vats bypass on google. I had to bypass, you simply measure the resistance through the chip, go to radioshack and buy the resistors that add to that amount or withing 2%. cut the orange wire that leads to the ignition and install the resistors bypassing the vats permanently.
http://vats.likeabigdog.com/
http://shbox.com/1/vats_bypass.jpg

Key must be made by the dealer and programmed to the vehicle. There is a chip in the key that the antitheft system must read to start the engine. Any key blank with matching cut can open the door, no chip necessary

I assume the fob is the remote door lock etc In short Yes you will have to return to dealer as they can match it by using your vehicle ID codes As for cost Not sure Shouldn't be too bad tho

no, you will half to get it towed to dealer and have a computer chip key cut from your spare key then thay will program it to the vehicle