When you select a folder (or document) you can enable the option to show all objects from all subfolders to make it easier to bulk-edit all your objects in the document. I recommend you check out this videos:
Regarding the default settings: make sure you also switch to the PuTTY plugin in the default settings before you set any of the putty defaults. Then it should use the default settings as configured for new connections.
Let me know if this helps.
Regards,
Stefan