Due to the lack of documentation on this process, I am writing my own tutorial. I may modify with screenshots later, but I'm a stay at home dad with two kids and a lot to do. Can't promise everything, but the text version of this should work for you.

Step 1 - Preparation
Step 2 - Software Setup
Step 3 - DO IT!

STEP 1 - PREPARATION

The things you will need:

HARDWARE
- NDS or NDS Lite system (I used a Lite)
- Your personal computer (I'm using a PC running Windows 7 64bit)
- NDS FlashCart or Slot1 Device (I'm using EZ-Flash Vi H[805] F[101] K[3.0 OB2])
- A game you want to back up your save from

SOFTWARE
- NDS Backup Tool Wifi (0.31f used)
- smallftpd (1.0.3 used)

Yup, that's it.

Make sure that your NDS is configured to connect over your local network (or router). Just play a game that uses Nintendo WFC, and edit the settings to use your access point IN THE FIRST NETWORK SETTINGS SLOT. If you already use Nintendo WFC, and your first set of settings are the one you use, your set.

STEP 2 - SOFTWARE SETUP

1) Download and extract NDS Backup Tool to your desktop. (The NDS file, and the INI file.) This is temporary.
2) Download and extract smallftpd to the location of your choice. (I used the desktop.)
3) Open your control panel and go to your network settings. (Network and Sharing Center for Windows 7)
4) Open your network connection status (for Win7 you click the network name link), and then click, "Details."
5) See the line that says IPv4 Address? Make note of this number somewhere.
6) Open the NDS Backup Tool INI File in Notepad or similar text editor, and you will see this:

Code:

#
# NDS_Backup_Tool_Wifi.ini
#

ServerIPÂÂÂÂ10.0.0.##ÂÂÂÂÂÂÂÂ! FTPd IP address
ServerPortÂÂÂÂ21ÂÂÂÂÂÂÂÂÂÂÂÂ! FTPd Service Port
#FileDirÂÂÂÂ/NDS_BackupÂÂÂÂÂÂÂÂ! Home Directory

FTPUserÂÂÂÂÂÂÂÂusernameÂÂÂÂÂÂÂÂ! FTPd Logon User name
FTPPasswordÂÂÂÂpasswordÂÂÂÂÂÂÂÂÂÂÂÂ! FTPd Logon password

SaveFileÂÂÂÂ0ÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂ! Saving size : 0:auto, nnn:Save File Size(KB)

#TrimÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂÂ! Rom Triming Backup

Now, where that ServerIP is, replace that number with the IPv4 Address you wrote down earlier. Keep the port 21.
Replace "username" with a desired username, and "password" with a desired password.
Save the file so it stays an INI file (shouldn't be an issue with Notepad) and load your FlashCart's memory card into the computer.

7) Copy the NDS and INI file for NDS Backup Tool into the ROOT of your memory card. When done, put it back in your FlashCart (which can now go back into your NDS or Lite).
8) In your C: Drive (NO SUBFOLDERS FOR SAKE OF EASE), create a folder labeled, "NDS_Backup."
9) Open smallftpd, DON'T CLICK THE PLAY BUTTON YET, and do the following steps:
a) Under Settings, go to GENERAL and make sure the port is 21. If not, change it to 21.
b) Under Settings, go to ADVANCED and click the Use Local IP tick box.
c) Under Settings, go to USERS. Here's the "hardest" part. Click ADD, and specify the login and password you chose in the INI file.
c-1) In the directories section, click ADD. Leave the Virtual Path as a / and in the physical path type c:\NDS_Backup.
c-2) Under Permissions click ADD, and leave the Virtual path as is, and make sure the permissions say, "LRW."
c-3) You can now click OK to save your user settings, and OK on the userrs dialog to go back to smallftpd.
9) You may now click the Play Button to activate your FTP!

STEP 3 - DO IT!

1) With your FlashCart loaded into your NDS, load NDS_Backup_Tool_Wifi.NDS
2) Once it connects to your network AND your FTP, it will ask you to swap your game card out for the one you wish to back up. DO NOT SHUT OFF THE POWER TO DO THIS! Press (A) to continue.
3) To immediately backup the SAVE of the current game, Press (B), then press (A) to confirm. It should start copying the SAVE over the FTP to the folder you created earlier. When complete it may say that the data transfer failed. Check your folder on your hard drive for the file. If its there, then you should be okay. (As long as it made it to 100%)
4) Rename the SAV file to match the name of your ROM, drop it into your FlashCart's SAVE folder, and load your game. It should work just fine.

Now, here's a breakdown of NDS Backup Tool. When you connect to the FTP, you can swap the cartridges out. Once you load the game to back up it will take you to the first "page" of options. If you already have SAV files on the FTP, you can update the one for your current game by pressing (A). You can press (B) to rip a new save, (X) will allow you to switch to a new game card, and (Y) will refresh the file list on the DS's end (in case you changed it on your PC's end). On this first page you can press  to get to the second page. On that page, the only difference is that (B) will ERASE THE SAVE FROM YOUR DS CARD! This is useful if you want to trade the game, but don't want the next owner to take advantage of your hard work.  again will take you to the third page, where you can rip that actual NDS ROM file. (This takes quite a bit of time, so if that's what you want to do, go get your charger just in case.) I think the third page would allow you to overwrite a SAV too, so if you download or modify a SAV, you can put it on the card like it was your own.

That's the method, the use, and some tips to do this. Hopefully now there won't be people stumbling from FTP tutorial to tutorial, trying a little bit of everything, and figuring out the simple answer through trial and error. (Yeah, that's what happened to me.)

I hope this helps somebody!