Configuration data is stored in 3 locations. Here is how to move all of it from MC12 to MC13.
1) Library field data (including user defined fields), views, sort orders, playlists, and podcast feeds are stored in the library (*.jmd) files.
To preserve these settings copy your MC12 library to the MC13 library location and open it with MC13. MC13 will automatically convert your MC12 library to the MC13 format the first time it is opened. Note that MC12 cannot open an MC13 library. By making a copy of the MC12 library for use by MC13, you can keep MC12 operational for a while in parallel with MC13. (I have done a lot of testing with recent MC13 builds and I am confident you can dump MC12 now if you wish).
2) Language file customizations, custom art, downloaded skins, and downloaded visualizations are stored in c:\Program Files\J River\Media Center 1x.
After installing MC13, use Windows Explorer to copy anything you want to preseve from MC12 to MC13.
3) Option settings, auto-import settings, favorites, toolbar customizations, skin selection, library location, and thumbnail cache location are stored in the registry and are unique per user account.
I have successfully moved all of these settings from MC13 on an XP system to MC13 on a Vista system by using regedit to export HKEY_CURRENT_USER\Software\JRiver\Media Center 13.reg on the XP system, copying this file to the Vista system, and double clicking it to import the settings into Vista.
Note that MC uses CR LF as a delimiter in Auto-Import registry settings, and CR LF is not preserved by regedit export/import. Therefore there is no way to move auto-import settings. You will have to enter these manually.
What I have NOT figured out is how to move MC12 settings to MC13 on the same system. I am pretty confident that you could manually copy important registry settings with regedit (from HKEY_CURRENT_USER\Software\JRiver\Media Center 12 to HKEY_CURRENT_USER\Software\JRiver\Media Center 13) but I do not know how to do this automatically.
In case you are not aware, you can run MC12 and MC13 at the same time. So what I did was open both and methodically copied all settings from MC12 to MC13.