Am I correct in understanding you wish to build an app that both connects to a new Alfresco repository and an existing non-Alfresco repository?
The route to take probably depends on what you need to achieve with your existing repo e.g. just retrieve meta-data/content or do you require search, version history retrieval etc. One option is to develop alternative implementations of the Alfresco NodeService and ContentService which talk to your existing repository. They can be plugged into our infrastructure to allow your application to retrieve from both Repository's via a common interface.
An alternative is to build a complete JCR adaptor, but this would be a lot of work.