The current (downgrades) of Pages v5.6.1, Numbers v3.6.1, and Keynote v6.6.1 are not based on the superset features found in their prior iWork '09 named counterparts. The upgrades to the iWork '09 applications ended in Dec. 2012. The current applications' document format has changed, and are now not backward compatible with the iWork '09 applications. If you open an iWork '09 created document in the new applications, and allow them to convert it, any unique features to iWork '09 applications will be removed, or mangled in the new document that just overwrote your original — if you haven't taken precautions.
Any iWork '09 applications that were installed in the Applications folder will be silently moved to Applications : iWork '09 folder on installation of the new applications. If the iWork '09 applications were installed from DVD, then they were installed into the Applications : iWork '09 folder originally, and no move is necessary. The original iWork '09 version numbers are unchanged, as they are entirely different applications.
If you had a Pages '09 Dock icon before the update, I would remove it from the Dock, locate your individual iWork '09 applications, and drag the ones that you want back to the Dock.
Additionally, the new application installation process looks in the old iWork '09 templates folder and if any templates are forwards compatible, they will be converted into the new document template formats, and placed in the new Pages, Numbers, and Keynote template location. The new applications do not support nested folders of templates.
Despite what you say, a proper OS X upgrade (not clean install) will leave your user folder contents unchanged — and that includes any iWork '09 documents that you had located there. We always recommend performing a full backup beforehand as a precaution.
No one in their right might upgrades an operating system while leaving applications running with open documents. If you never saved that document once to trigger autosave in the iWork '09 application, then that document is lost for good.