Jeroen,
We haven't really dealt with that before, but I have something that may work for you. You can easily set the app id and app secret using JFBConnect, it's important to make sure you reset it back to the JFBConnect keys when you're done. That way, if JFBConnect needs to make any calls later, they won't fail (or go to the wrong app).
So, code like below should work for you as a wrapper for you:
$jfbcLibrary = JFBConnectFacebookLibrary::getInstance();
$fbClient = $jfbcLibrary->getFbClient();
$jfbcAppId = $fbClient->getAppId();
$jfbcSecretKey = $fbClient->getAppSecret();
$fbClient->setAppId('12345');
$fbClient->setSecretKey('xyz');
// ADD YOUR CODE HERE. Can use $jfbcLibrary->api(...) as normal
$fbClient->setAppId($jfbcAppId);
$fbClient->setSecretKey($jfbcAppSecret);
The other think that you'd likely need/want to do is in the /components/com_jfbconnect/libraries/facebook.php file, edit the api and rest functions. In both, you'll see:
$params['access_token'] = $this->facebookAppId . "|" . $this->facebookSecretKey;
Change those to:
$params['access_token'] = $fbClient->getAppId() . "|" . $fbClient->getAppSecret();
That will make sure the 'current' app and secret keys are used in those calls.
Whew, hope that helps get you going. Should you run into issues or have other questions though, just let us know.
Thanks,
Alex