You will need to set the correct permissions for each set of credentials used to collect data.
The permissions required can be found in the UCCS Analytics Deployment Guide in the section "Credential permissions needed to collect data from different environments"
To use multiple credentials you need to set-up multiple data collections.
In the UCCS Analytics web interface go to Admin Settings > Data Collection
In the Data Collection section you will only see one Exchange Configuration data collector and one Mailbox Contents data collector
Click the (+) plus sign to create additional data collectors
For the first collector you could specify subset of your users as the targets and one set of credentials and next collector could specify a different subset of users as targets and a different set of credentials.
With each data collector configured you can specify different Targets and different Collector Credential