My personal suggestion would be to implement watch rules for changes to system/service configurations (i.e. /etc), changes to scheduled jobs (i.e. /var/spool/(cron|at) ), and kernel [/module] changes (i.e. /boot). Malware also likes to put stuff in /usr and /lib* so consider watching for writes there too. Keep in mind that when updates are installed it will generate a large number of events. If you have services that write to these paths frequently it could DoS the machine and considering auditd's default behaviour is to halt the machine if the filesystem it's attempting to write to fills up, I suggest careful testing in non-production environments.
Finally, if you can't fix an SELinux policy issue, don't disable it; instead, change it to permissive.
Here's my disclaimer for this advice which is basically a modified MIT license:
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