Ok, so you went whole-hog and now have a nice DS-capable flashcart and either have FlashMe v7 installed or are using one of the many passkey devices.
But how to get those savegames you have on your carts down onto the flashcart for use with the ROM?
Simple. Just download and install ReinMoon!
It can seem daunting when you first run it because EVERYTHING will be in Japanese if you did NOT modify the config file that's in the Reinmoon directory on the root of your flashcart.
It comes with an easy-to-understand auto-installer as well...matter of fact, that's pretty much the ONLY way to install it.
Make sure the cart you want to backup the savegame from is in the DS Slot and boot from the flashcart in DS mode.
Run Reinmoon after configuring it to use English and then just press START + SELECT at the same time and it will ask you to press START when you want to begin backing up the savegame of the inserted slot. Most of the time the program will actually KNOW what cart is in there and name it, but sometimes it doesn't recognize the newer carts as the savegame data for those carts might not be in the Reinmoon cart list file just yet.
After pressing start, just wait. It will tell you when it's finished.
Once it's done you then have a flashcart-compatible savegame you can use with your ROM!
All you have to do now is rename the savegame to the same name as the cart. For us Supercard CF/SD/mini-SD users you will have to use the suffix ".nds.sav" and delete the original savegame file that was created when you patched the ROM using the Supercard software. You can either hook the card back up to your computer or use the DS Organizer homebrew to rename the file right on the DS itself as well as delete the old savegame.
I've tested this with Metroid Prime Hunters, Animal Crossing, New Super Mario Bros., Mario Kart DS, and the rest of my collection. Worked like a charm with no problems.
It's a hell of a lot easier than using that damnable DS Max Duo hunk-of-junk to backup the gamesave from the cart to your PC, then uncompress and then run it through a homebrew converter to turn it into a flashcart-compatible gamesave.
I found a slew of DS carts that didn't like that converter, so using Reinmoon is more reliable.