I had the requirement from a Custom Cron task and I came across this so thought of sharing.
I wanted to add Workorders from my Cron based on the SiteID I was passing as a parameter. So, for each site I have a Cron instance.
What I did was use the setInsertSite, setInsertOrg method on the MboSet class.
So, before calling add I set the relevant SITE and ORG and then called add so it makes sure that only the appropriate sequence or autokey (based on site and org passed on MboSet) is updated.
Can be very useful in some scenarios so thought of sharing.