Yes, migration-center offers several ways to split a source repository into two or more target repositories.
Let us assume that you want to split your source repository S1 into three target repositories T1, T2, and T3.
You could then define three different scanners in migration-center, one for each target repository. Configure each scanner to only scan the folders or documents that you want to migrate into the corresponding target repository. Then use the regular organize, transform, and import features of migration-center to migrate the documents into the target repositories. Done.
Another way is to scan the entire source repository and then use migration-center's organize feature to split the scanned objects into several migration sets. You can use powerful filters to select exactly the needed documents into the migration sets. After that use the regular transform and import features of migration-center to migrate the documents.
Which way to use depends mainly on the capabilities of the source system scanner and on the amount of documents to migrate.