The kongregate accounts can be used from any launcher if you follow a simple method. Some time ago a player posted how to do this, but for those who do not care to look you need to make a .txt file called Extra.txt
You need to type this into the file and save it into your spiral folder or steam folder or in the contents folder in the case of the standalone launcher.
You will need to use something to inspect the kongregate shell for spiral knights to find your id and authentication token. The token is found usually right after your ID. You will have to have the play now window up inside the shell so it that your account data will be shown.