I have no experience with that specific app, but most apps use configuration mechanisms that will find their configurations no matter which app they reside in, which means this specific app may find values in
etc/apps/workday2/local/api.conf and merge the configurations.
What you will probably need to do is install the app on two separate splunk instances that each send their outputs to your indexers.
Thank you for the quick reply. That makes sense - it's too bad, since most Workday clients have multiple tenants and we have different event logging needs for each tenant. We don't have separate indexers or instances at this time; just one instance that is the application and the all the indexes.