We have our own SQL Server membership database for our ASP.NET application and maintain an "online" status of all our members in the database. I don't see a way to override the built-in Messenger functionality that determines when a user is online. We are not using the CuteChat database for our users so LastLoginTime is not applicable.
Secondly, if a user were to be online but not have the messenger window open, they will not know they have a message until they open the messenger window. Is there a way to have the message window pop up or some sort of popup notification that someone is currently messaging them via chat without them having to have the messenger window open?