A Macbeth said, your saves will continue to work fine. I started my first game in the unpatched version, and installed the hotfix and latest
patch during that game.
Some story fixes and changes in the patch only apply to new games (for example, Finnigan in the cellar of the Ducal inn carries a much better selection of stuff for sale in games started after the patch is installed), but your current game will benefit from the technical fixes, extra quicksave slot, etc.
