RSA Key question

I believe I understand KB article 10477 on how to get the keys, however it really does not go into details on what it does.

Does settingthe key need to be decrypted for each query to the database or is that all handled via IIS?


If I run aspnet_regiis toencrypt the connectionstring section of my web.config file, if I add a new connection string do I have to decrypt the file and then add my new connection string and if so how do you re-encrypt the file with the same settings?