So, I had two questions, but I figured out the first: As it turns out, if you create a domain in SQL Developer Data Modeler and you want to apply a CHECK constraint, you need to use %COLUMN% to represent the column. This will be replaced when you engineer your relational model.
(To be clear, in Data Modeler Tools, Domains Administration, Add a domain, the click Check Constraint.)
That works, so here's the second. Does anyone know why domains aren't saved with the model? They are, apparently, stashed in an XML file just under the datamodeler binary directory, e.g., c:\program files\datamodeler\domains\. You can export them, but I'm wondering why Data Modeler treats domains differently from other types (distinct, structured, collection, etc). The docs don't say much beyond transcribing the various dialog boxes.
I suspect that the reason they are not stored with the model is for reuse. Usually an organization will want to have standards. And if you've spent a lot of time setting up domains for one application, do you really want to have to maintain common domains in multiple places?