Not sure whether you already know this or not...
I think a typical step for using 3-in-1 is first to run the dumper application (which you put in the flash cart), then the application will ask
you to switch the cart in slot 1 (i.e. you need to put the game/retail cart now), and it will read the content into the 3-in-1 cart (in slot 2).
After it copies the chunk of 32MB, then it will ask you to turn-off DS, and swith back to flash cart in slot 1 and rerun the dumper application.
Once you rerun it, it then copies that chunk of 32MB from 3-in-1 cart to the flash cart. This process should be repeated as many as
needed when the size of the game cart or savegame file is more than 32MB. At the end, the dumper application will combine those
chunks of data in the flash cart accordingly.
As far as I could recall, you could prepare or set-up a folder in your micro-SD card to hold those temporary chunks of data.
And the final compiled file will be in that folder as well.