Skotea,
As I mentioned, I do not use any security like this so I have limited knowledge of this area.
In FlexViewer 2.1 I would say that the best way to handle a portion of the security is to use different config files. The issue you will have to overcome there is how to prevent access to a more privileged config file. I have heard of so handling this through a ASP.net front end that directs a user to a particular config based on login and access to the IIS directory that has those config files is protected through windows authentication.
If you secure your map services using ArcGIS Manager than in Flex you will have to use tokens to consume them. You will have to modify the FlexViewer to handle this. I can not give you any advice on this but I know people have do this in the past and posted on the forums so just search for "using secured map services" or something along those lines.
There is no out of the box or standardized method to do any of this using FlexViewer, so you will have to develop this methods your self along with the code.
Once again I am not expert on this and have no experience in this area. I just came across that article and though I would pass it on.