ORM Designer supports Mapped superclass as much as it is possible.
It depends on ORM (Doctrine or Doctrine2) and format you're using (XML, YML, or Annotations). For example for Doctrine2 and PHP code:
/** @MappedSuperclass */
/** @Entity */
class EntitySubClass extends MappedSuperclassBase
There is no annotation which define that EntitySubClass is defined from MappedSuperclass. But in this case, ORM Designer also parse extends keyword and after few hacks can attach MappedSuperclass with EntitySubclass.
Unfortunately in YML/XML code, there is no way how to get this information. XML definition of mapped superclass and derived entity looks like this:
<id name="id" type="integer">
<field name="age" type="integer" nullable="true"/>
And as you can see, there is no mention about relation between entity a and entity b. This relation is available only in PHP code and if you're using ORM Designer to import XML/YML, this is one of the few information (I think it's only this one) which can't be imported directly.
For this cases you need to add this inheritance manually to your model.