Found this information on Steam. The conversion from Games to windows live has been accomplished but for those of us with saved data, this process should fix you up:
shoupinou [developer] Dec 15 @ 9:07am
HOW TO: Replace Games for Windows Live functionality with Steamworks functionality in Dark Souls™ Prepare To Die Edition for PC
You can now update your Dark Souls™ Prepare To Die Edition for PC game to replace the Games for Windows Live functionality with Steamworks functionality. The update is available from today – December 15th and will let you keep both your Save Data and Achievements.
If you played or are currently playing Dark Souls™ Prepare To Die Edition, you will be able to update and keep your Save Data and Achievements. The Save Data and Achievements transfer service is being provided from December 15th to February 16th. From February 16th, the new version using Steamworks functionalities will become the default version of the game.
Please read the process below to update your game properly. Please note that from February 16th, we cannot guarantee that your Save Data and Achievements will be able to be transferred.
CASE 1: If you already purchased Dark Souls™ Prepare To Die Edition prior to December 15th, the following process will be available to February 16th for you to transfer your Save Data and Achievements.
For users who purchased a Game for Windows live version from a retailer (Disc) or Games for Windows Live Marketplace (Digital):
We recommend that you add Dark Souls™ Prepare To Die to your Steam account using your serial
Launch the game and connect to Games for Windows Live.
Run the game (only the currently signed-in user’s Save Data and Achievements can be transferred to Steam).
Close the Game.
Right click on your game in the Steam Library, go into Properties, check that the BETA tab is set to “dsptde-2.0-“
Launch Dark Souls™ Prepare To Die Edition v2.0 from Steam
The game will look for previous Save Data and Achievements. If Save Data and Achievements are detected on your computer, you should be able to continue your progress in the game. Achievements should be unlocked in Steam.
For users who purchased a Game for Windows live version from Steam:
Launch the game and connect to Games for Windows Live.
Run the game (only the currently signed-on user’s progress can be transferred to Steam).
Close Games for Windows Live
Right click on your game in the Steam Library, go into Properties, check that the BETA tab is set to “dsptde-2.0-“
Launch Dark Souls™ Prepare To Die Edition v2.0 from Steam
Sign in using the same live profile used in step-2 to import your Save Data and Achievements from the Games for Windows Live version to the Steam version for the same profile (gamertag)
The game will look for previous Save Data and Achievements. If they are detected on your computer, you should be able to continue your progress in the game and achievements should be unlocked in Steam.
CASE 2: For users who purchase Dark Souls™ Prepare To Die Edition between December 15th and February 16th:
Once the game is downloaded, right click on your game in the Steam library, go into properties, check that the BETA tab is set to “dsptde-2.0-“. The game may ask you to create a Game for Wwindows Live Account, simply discard this request
Launch Dark Souls™ Prepare To Die Edition v2.0 from Steam.
CASE 3: For users who purchase Dark Souls™ Prepare To Die Edition on or after February 16th (this will be the steam only version):
Just Launch Dark Souls™ Prepare To Die Edition from Steam
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