Hi HARDBEAT. Here's a step-by-step walthrough:
As stated in the readme of Rudolph's 3-in-1:
1. Create a folder in the root of your slot 1 flashcard named GBA.
2. Inside GBA, create another folder called Save.
3. Copy 3in1_exppack_tool.nds in your root (or wherever you place your nds roms.
Now this is one very important step that everyone seems to forget to tell you. Without it, you wouldn't be able to save your progress in games:
4. Install GBATA.exe in your PC (you can download it from the GBATemp repository and it works perfectly with Wine in Linux).
5. Open GBATA.
6. Open the GBA rom you want to patch (see we haven't copied ani GBA rom in the flashcard yet).
7. Chose the SRAM Patch tab and patch the GBA rom (my guess is that if the Patch button appears greyed out it's because the rom has already been patched by its release group.
8. Rename the resulting output_rom_foo.gba if you prefer a different name and copy it in your GBA folder in your slot 1 flashcard.
Now everything's ready to play your rooms and be able to save:
9. Start your loader as usual (you know, push the ON-OFF button in your NDS).
10. Open 3in1_exppack_tool.nds.
11. You have three "tabs" here and you can switch between them with your L and R buttons. The first one handles rom running from your SRAM and is the fastest and most comonly used option. The other two are to load games more permanently into the NOR of your EZFlash V (necessary for heavy games like Chain of Memories or the new Spyro and for Pokémon and the last one id to enable rumble mode (if only more NDS games supported it, 'cause I love it).
12. Chose a rom in the upper screen and load it into the SRAM (it should take around 30 seconds and you have to do it every time).
13. Run the rom if it's not running already (I think you have a button to load it, then another to load it + run and then another two to perform some operations with the save file but I'm not so sure how these work and they're not really necessary).
14. While the game is running, the save will be performed just like it was a regular GBA game wether in checkpoints or automatically, you just don't have to worry about that anymore.
Enjoy!