Knowing the solution, it seems quite obvious, but it took a while to track down the proper syntax.
In this example I have a custom CForm which contains a few different $model properties, in addition to the base form data.
To call the validation on multiple models in the form, simply modify any calls of
CActiveForm::validate($model);to use an array of models as the first parameter as such:
CActiveForm::validate( array($model, $model->subModel, $model->subModel2) );