Search operations use the namespace associated with a context passed to them when they are called.
To perform an operation in a namespace, wrap a context with appengine.Namespace, and use that context when calling methods on an index. You may see an example in the "Using namespaces with Search" sub-chapter of the "Implementing Multitenancy Using Namespaces" online
document.
This is the usual way of performing operations in a namespace, and would require one index in your situation.