You can buy the key from eBay and give it to your local locksmith, along with your valet key. Many can also program them. I would just buy one from the locksmith, this ensures you get the right one. Many of them are not that expensive, although, the ones with the remotes built in are.
Programming of new keys will erase the lost keys, which is what you want. Your valet key will need to be reprogrammed .
If your key had the remote built into the head of the key, I can see you looking at $300-$350 when all is said and done, maybe more. If you replace with regular keys, no remote, but still with transponder chip, $200-$250 would be about right. Maybe less.
For 2006 Honda Civic, both the keys and remotes can ONLY be programmed with special diagnostic equipment. A locksmith or dealership will have the equipment. There is NO on board programming of these vehicles. You CAN resync a remote after battery replacement by holding lock and unlock, but as far a programming a new one, locksmith, dealership, in that order.