I always begin the editing process from the PSE Organizer, regardless of which editor I will use, whether PSE9 or PS CS5.
A very nice feature of the PSE Editor is the ability to save a file as a member of a Version Set in the PSE Organizer. Problem is, for some edits PS CS5 has features that PSE lacks but PS CS5 does not offer the choice of saving a file as a member of a Version Set.
So here is how I've resolved the issue of wanting to created a Version Set after editing with PS CS5:
--do a Save As of the edited file so as to leave the orginal untouched
--open the Organizer and you should see the just-saved file on your screen
--open that saved file with PSE
--if you wish to add Styles (bevels, strokes, a frame, etc.) but did not so so with PS CS5 (PSE has some Styles that PS CS5 lacks and vice versa), add the styles in PSE
--save the completed file as a Version Set by choosing the relevant choice in the PSE Save As dialog box