[MlMt] Setting up SS and MM: mark messages as Not Junk?

[Sparky Doosan]

I'm reading http://c-command.com/spamsieve/help/setting-up-mailmate and 
got to the statement:

The Mark messages as Not Junk if score is below setting does not affect 
SpamSieve or its filtering.

Rather, if SpamSieve thinks a message is less spammy than the score that 
you enter, MailMate will tell the mail server that it’s not junk...

Again I apologize for trying to come up to speed quickly, I'm sure this 
is well-documented somewhere but still I ask... what does "MailMate will 
tell the mail server that it's not junk" mean?

I suppose a better question would be, is there MM equivalent to 
http://c-command.com/spamsieve/help/using-spamsieve ? I mean I do see 
the excellent Introduction in Help but the statement in question seems 
to suggest I haven't set up my server IMAP folders correctly yet. My 
other recent question (and quick answer, thanks again) points this way, 
I needed to get my Sent folder properly configured.

Thanks!