Either FreeS/WAN would have to set-up a repository on their website, or somebody with a respository would have to add the apporpriate RPMs to theirs. There was recently a thread about repos'ies... Maybe search for it and check them.
I'm not too sure about it, but I would guess apt looks through the RPM database to see what is installed, and then compares that to the lists it get from the repos'ies. So, it should be able to recognize anything you install manually and upgrade it if a new version shows up in a repos.
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