First, the version 5 files are copied on top of the version 4 files so that you only have one directory when finished.
The only output locations I know how to change are the ones for where the Sony LRF files will be stored (under the save file as area in the Make eBooks|Sony Reader box) and the File|Save File As to save a source copy.
What is interesting is that there is not an option to save the file as a BookDesigner file. BookDesigner uses an extension of HTML0 (that's a zero at the end) and can be seen in the TMP area in the BookDesigner directory of Program Files. The HTM or HTML save options produce a file of exactly the same length and content (as reported by Ultra Compare.)
To get back to the editor mode click Configuration from the top menu bar and then select Editor/Reader Mode. This will return you to editor mode. (I got there once and do not plan on returning to reader mode again.
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