Apply the following steps for using a new DITA Open Toolkit:
Edit your transformation scenarios and in the "Parameters" tab change the value for the "dita.dir" directory to point to the new directory.
If you want to use exclusively the libraries that come with the new DITA Open Toolkit you have to go to the "Advanced" tab, click the "Libraries" button, uncheck the checkbox "Allow <oXygen/> to add high priority libraries to classpath" and configure all libraries that will be used by the ANT process.
If there are also changes in the DTD's and you want to use the new versions for content completion and validation, go to the <oXygen/> preferences in the Document Type Association page, edit the "DITA" and "DITA Map" document types and modify the catalog entry in the "Catalogs" tab to point to the custom "catalog-dita.xml".