Sadly there is no readme, which is something I've been asking for since I found this app. Without one. its not clear how to get the app running. For some reason Pokedoc adds the folder/directory name (savegame_manager_0.2.1) to the beginning of the file names (Ex savegame_manager_0.2.1\savegame_manager.nds). This causes problems as the NDS file looks for "savegame_manager.ini", not "savegame_manager_0.2.1\savegame_manager.ini". You need to rename both the NDS and INI files to "savegame_manager". Place them both in the same folder, and then boot the NDS file. It should work after that. If it says it can't find the ini file, move it to the root of the card and try again. Once the app actually loads, its self-explanatory. If you want to do a dump via Wifi, you will have to ask someone else about it as I have no idea how it works.
A heads up: Ignore the releases in the first post and use snapshot 2 (found in post 76). It is the most recent stable build. It works with a 3-in-1 (tested it myself), but Noko is having problems copying saves back to a retail cart.
Yup!
Goodie. Thanks for the heads up. Sucks you lost your save on the retail cart. Thankfully it is backed up so when the problem is fixed, you restore it. Hopefully Pokedoc gets back to us this weekend about bug fixes.