SpamSieve ignoring Apple Mail rules ?

As a new SpamSieve user on Mac OS 10.7.1 Lion, I am impressed by its efficiency, yet there seems to be no way one can prevent SP from sorting out mails already submitted to Apple Mail rules (other that junk rule, obviously).

Thus mails that should require special attention find themselves stacked into the Spam box instead, with the risk of having them go down the drain unnoticed.

Barring possible insuperable programming difficulties, I don’t quite see the logic of spamming mails that the user has explicitly pointed out as worthy to be read already.

Did I miss something in the Help section (my English not being quite what it used to be), is it a program shortcoming and, if yes, can we hope for an update which will put things together?

The normal setup for Apple Mail suggests putting the SpamSieve rule at the top of the list. This allows SpamSieve to screen all of your incoming mail for spam. If SpamSieve puts a good message in the Spam mailbox, you should correct the mistake, and it will learn to recognize messages like that as good in the future. If you know for sure that certain kinds of messages will never be spam, you can change the rule ordering to put those rules above the SpamSieve rule.