Skyrim does not manage your save files between different characters very well. I've ended up having to switch the Saves folder between characters. I've written up this program to handle that process for me and anyone else who would like to use it.

When you create a profile, it creates a folder for that profile and copies your saves to that folder. When you load a profile it takes the saves in that profile's folder and moves it into the main skyrim saves folder.

Note - This does not interact with the game at all. I'm not automating or scanning for new save files during play to update the folders. This is something to do before starting up Skyrim.

.net framework 3.5 required.

Instructions:
1. Download the Skyrim Saves Manager.exe and put it anywhere you like.
2. To be safe, backup your Saves folder.
3. Run the Skyrim Saves Manager.exe and set the paths you want for the Profiles, Backups and Skyrim Installed path if you'd like to launch Skyrim from the manager.

Updates:

version 1.2
1) Added a "Save to Profile" button. This will first backup the profile folder, then synchronize your main Save folder with your current profile (copies any new files in the Saves folder to your profile folder and removing files from the profile that no longer exist in the Saves folder).

version 1.1
1) Select File instead of just directory for the Skyrim Launcher.
2) Added feature to copy individual files between the currently loaded profile and the selected profile.
3) Loading profiles should work with Profile Paths set on a different hard drive.