In PL/SQL Developer 14.0 you can use the Workset feature for this. See chapter 15 in the User's Guide:
15. Worksets
A workset is a set of Program Windows, SQL Windows, Test Windows, Command Windows, Report Windows and Diagram Windows that you are working on. Changes made to these windows are preserved when closing and reopening PL/SQL Developer, even if you have not explicitly saved or compiled these changes. After finalizing your work you can apply the workset, so that changes to the files and database objects are permanently saved.
A workset holds the window contents, sizes and positions. When a workset is reopened later, windows will be restored exactly like they were previously used.
All workset-related functions are accessible from the Workset group on the File ribbon.