Where do I put the scripts? What on the mail server must I edit?

The answers to that question depend on the architecture of your mailer environment. You mentioned Lotus Notes. How does Lotus Notes handle its mail queues? If you have the opportunity to have LN store incoming mail into a queue directory where a script initiated by cron can "pick it up" and then hand it off to a delivery agent then that's one way.

SpamAssassin is actually invoked by the MTA through a socket. Can LN deal with that? Can procmail be invoked by LN?

Short answer is: it all depends. You need to work with your MTA administrator to work out the naughty bits of getting this to work.