I have 2 bamboo instances with different sets of users.

[Gbowe]

 Which groups do I use in JIRA-Crowd to auth each.

The default group is bamboo-users which I have been using on our long time running instance of bamboo. We now purchased a new instance of Bamboo for a different group but they will authenticate via the same JIRA-Crowd. Can I setup which group the new instance users for its users?

[Timothy]

I think you should create another JIRA User Server to handle your second Bamboo instance. Though, the same users, groups and memberships will be used for both Bamboo instances. 

Can I setup which group the new instance users for its users?

Create a new group in JIRA called bambo-users-new and use this new group in the 2nd Bamboo's permission architecture.

[Gbowe]

Thanks Timothy. So login still requires membership to bamboo-users right? And then I would set permissions on build plans based on my new list of users?

[Timothy]

No. Login requires the user to be granted the Access Bamboo permission (https://confluence.atlassian.com/display/BAMBOO/Granting+global+permissions+to+users+or+groups) no matter which group you create in JIRA.

[Gbowe]

Excellent. That works great. Thanks again Timothy,