If I understand your question, you want to use the Flash Access Manager and/or the Watched Folder Packager (both are components of the Reference Implementation) to package content for a license server that uses Custom Authentication. To accomplish this, you need to use the Flash Access SDK to create a policy that specifies Custom Authentication is used. For example:
Policy pol = new Policy(false);
LicenseServerInfo licServer = new LicenseServerInfo(AuthenticationType.Custom);
// set rights and other policy attributes
Once you create the policy, place the policy file on the Packager Server, and you can use this policy to package content.
If licenseReq.getRawAuthenticationToken()==null, that means the client did not include an authentication token in the request. Please refer to the links Eric provided in this thread for information on how to specify an authentication token using the client side APIs: http://forums.adobe.com/thread/854472?tstart=0