Firstly, all BPMN elements can have eaDocX Profiles. You just have to find out which ‘true’ meta-type they are stereotypes of. Most BPMN things are stereotypes of ‘Class’, but there are also other meta-types. To find out, just create ‘Quick Document’ from the package, and eaDocX will figure out all this for you.
AS for the rest of your question, I’m not sure which bit is an EA problem, a problem with your model structure, or and eaDocX problem.
I suspect a bit of all of them.
When I’m teaching people about modelling, I usually tell them to avoid the structure you have: a package, with lots of different important things in it. You have Use Cases, and Processes, plus I guess other stuff related to these two. I always say to create sub-packages: one for the use cases, one for the processes. Tidier, and easier to manipulate.
