Generally, using multiple purecloud orgs within a single Salesforce environment poses no special concerns. The client utilizes the standard implicit grant login flow, meaning it simply authenticates on behalf of a user.
Using different configurations for different users is supported by way of the user's membership within a call center definition; simply create additional call centers and associate users with them to provide different configurations for those users.
Where things do get a little more complicated is for features that utilize a server side login (specifically the email routing and campaign management features). The authentication these features use is scoped to a single org. The integration only supports a single oauth client for these two features, meaning they can only be used with a single purecloud org.
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Richard Schott
Genesys - Employees
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