Thank you for your post.
I'm a little confused. If your primary keys are linked to your foreign keys, "but the foreign keys don't show up in the related tables", does that mean the foreign keys are not present? Does that mean the foreign keys are there but they don't match? Is the foreign key field unavailable for display?
Somewhere in your "Software" table, you need a key that links to the "Employee" table. Is the key field a "Software" ID or "Employee" ID? That is, how are you linking the software to the employee? If you are in the Employee database and viewing the software, you should be able to sort each portal by the software vendor.
Any additional information would make this easier to understand. If you want to send in your database file, I am happy to look at it. I have sent you a private message (top of this page - right side - X Messages) with instructions where to send the file.
Sorry I can't be of more help.