Sorry this is kind of an entry level question, but...

In the Wiki pages on SpamAssassin, I see it recommends using /opt/zimbra/conf/salocal.cf.in for SA customization. Meanwhile, in many of the forum posts, some of the more authoritative poster on the topic seem to mention customizing /opt/zimbra/conf/spamassassin/local.cf.

Is one a better choice than the other for any particular reason?

I hate to say it, but spam seems to be the place Zimbra needs the most work. I feel like I'm getting the worst of both worlds... I'm having to go in and do a lot of manual management of SA & postfix, but it's in a packaged piece of software so I'm having to muck around with files with often-mysterious locations/interactions and that get re-written with each upgrade.

Even if there was just a place in the gui where you could manually enter specific variables for postfix/amavis/sa, that would be a big improvement!