If you choose to open your stationery documents in any way except the new document dialog box in ClarisWorks 3.0, then you will need to manually change the radio button in the Save dialog box from "Stationery" to "Document." This applies only to the first time the document is saved.
Once the stationery has been opened in any manner other than the new document dialog, then it will NOT default back to "Document" in the save dialog (even if accessed through the new document dialog) until you quit out of and restart ClarisWorks.
This includes creating new documents created from stationery from the open dialog box or an alias. This did not occur in previous versions of ClarisWorks.