You can use EJB 2.1 and 3.x in parallel, we also have that in an application which is quite some years old and still not completely migrated.
For the old parts, you still need the same setup with all the deployment descriptors, as @bkail pointed out.
But if possible, I would strongly recommend not to mix up things if you have the chance to create a modern JavaEE 6 based application. Better try to interface with the old parts which are still needed and keep it as a separate application and use old EJBs or introduce a temporary interface between old and new application until it is migrated.