Okay I figure I'll make a little guide since people are somewhat confused as to how to use this application.
1)First thing you need to do is setup an FTP server. I have my own private FTP server overseas but I imagine smallftp would work just as well. Verify that your server is working on an open port (usually 21) by connecting to it with a client like http://filezilla-project.org/. If you need specific help with what programs you should use and what you need to setup an FTP server it's quite easy to google as there are literally thousands of FTP servers out there. Although I hear for the purposes of save file backup smallftp is the best. Once you verify your server is running be it smallftp or whatever it is you use AND you've verified you can connect to your server move to step 2
2)Verify your NDS can connect to the internet normally go onto the official Nintendo GTS and setup your wifi connection in the wifi connection settings of your NDS. You will have to set it to your home network and verify your NDS is visible by your router on your home network. Once you verify your NDS can use your home network to go online AND you see it can access the official (Nintendo based) GTS and function normally move to step 3. Again if you have trouble with this the official Nintendo support website has instructions on how to get your DS working on your home connection.
3)Now we need to setup the save manager. I'm using an Acekard2i and copied over savegame_manager.ini and savegame_manager.nds to the root of my acekard. Now that you have these two files copied to the root of your acekard2i we need to modify the configuration settings to redirect our save files to our personal FTP server.
4) Crack open the savegame_manager.ini you just copied and that is in the same directory as your savegame_manager.nds and you'll see this:
Simple fill in as required
If you're running small ftp or some other home FTP client you need to redirect savegame manager to your home computer to do this you'll need your home computers IP address. This can be found by hitting start and in the search programs and files box or the run box typing cmd.exe
now that you have cmd.exe open type ipconfig and you will see the IP address of your home computer running the ftp server, it's usually something like 192.168.X.X
ftp_ip = ftp.myfakeftpaddress.com or (192.168.X.X ) < your ftp address
ftp_user = yourftppassword < Make you set the password in your FTP server to exactly what you set in your FTP server settings A good rule of thumb is that if you can login with filezilla with the exact username and password you type in here to your ftp server your savegame manager will too.
ftp_pass = yourftppassword
ftp_port = 21 < your ftp port again, if you can login with filezilla using this port so will savegame manger.
Save the file, close it and boot up your flashcard with the program copied over.
5) Run savegame manager.nds and press B at the start screen be sure not to have any GBA games in the slot below if you have an older DS.
6) We need to first obtain a copy of our save file so we hit backup game> .sav on the touchscreen.
7)It will instruct you to remove your flash card and insert your retail game when done hit A
8)If you setup steps 1-4 correctly it should only take 12 seconds or so to connect to your home FTP server. If you messed up steps 1-4 or something on your router and/or computer is blocking your ftp server or NDS you will get an error at this point. error list below
A)stuck at connecting to FTP... < your FTP server is not setup correctly see if you can connect to your FTP using programs on your computer
B)Stuck at connecting to AP< Your NDS cannot connect to your home connection see offical nintendo support as to why
c)Incorrect password< your ftp password is wrong
9)If all goes well you will notice three options A, select a savegame to overwrite already on your FTP server. B move one folder up in your FTP server or press L+R to create an entirely new copy of your retail HG/SS savegame on your FTP server, I recommend you use L+R. You will then see a progress bar and your savegame will begin to download to your FTP server folder.
10) Turn off your DS, your savegame is now on your PC!
11)Once edited savegames can return to your DS by repeating at step 7 and instead touching the restore .sav>game
12. Use your D padto select the save file you want to restore and hit A. Follow the same instructions.