With your MailScanner Front-End Service, is there a way to teach or train the system what is spam and what isn't, when there are false positives or false negatives?

Yes, as the server administrator through the root access in WHM you will have access to MailControl which is included as part of the MailScanner package. MailScanner can be configured such that all email is stored in the quarantine directories that MailControl accesses so that you can then teach SpamAssassin through it's ham/spam facility when it passes a false-positive or false-negative email on. However, normally it is not necessary to manually teach the spam filtering system as it automatically learns as mail goes through the system.