@keegan_oconnor There's a place in the SSO settings where you can specify which homegroup to put them in. Under the classic system (if you have not yet migrated to admin console) it's under Map User Attributes and you just select Home Group and choose a home group.
All of our users are added into one home group called "new users" for example.
From here, you can decide what you want to do with them. There are at least 3 alternatives, maybe more.
1) Use Fusion to perform some queries about the user and automatically reassign their home group based on your findings.
2) Run a report regularly and assign all users in the "new users" homegroup to another homegroup.
3) Tell all users to fill out a profile update request assigned to admins, and based on their answers, you'll know where to put them.