There are "all-in-one" files there contains more than 1 amiibo. You can import them to Flashiibo Pro, and have them organized by amiibo series automatically. To do that, follow the instructions below.
First, make sure you are on firmware version 52p or later.
The process takes very long time, so please keep the Flashiibo Pro charged.
You can use either a premade all-in-one file (here is an good example), typically named something like "ally-all-in-###.bin" or "###-in-one.bin". Or you may use the all-in-one creator to make one yourself. (all-in-one creator was made by @alup2740)
[IMPORTANT] If your all-in-one file has a long name, and the rolling animation starts to play on the file name, you should shorten it. It's easier if you rename it before uploading it. In general, it is recommended to keep it within 15 characters. A good strategy is to name it "###-in-one.bin"
Follow the "Using PC / Mac" section above to upload the all-in-one file.
On Flashiibo Pro, go to File Explorer.
If you already have a folder named "_all".
You can delete it by press-and-hold OKAY and choose Delete; that will give you a fresh start. It will take a few seconds.
You can also keep it. A future import run will just add missing files if the previous import was interrupted somehow.
Find the recently uploaded all-in-one file, and press OKAY on it. Don't press more than once.
The import process starts, it takes between 15 to 20 minutes. The screen will appear to be frozen and the device doesn't respond to button presses, but that's expected. The blue light will start to blink once every second. Each blink indicates one file import.
At anytime during the process, you can press and hold both UP and DOWN buttons at the same time for 1 to 2 seconds to cancel the import.
During the time the blue light might become constantly on and no longer blinks. That's usually because the device becomes fully charged. You can remove the charger to see the blinks again.
Upon on completion (about 15 minutes) or cancellation, a screen will show up telling you how many files have been imported (typically 800+). All files will appear under a folder named "_all". They are organized by amiibo series. That means the The Legend of Zelda amiibos in the Super Smash Bros series will not appear under the Legend of Zelda folder, look for them in the Super Smash Bros folder instead.
If you used the "good example", your storage percentage should be around 70% with the all-in-one file, and 45% the all-in-one file itself is deleted. You can find the storage percentage under settings. If the number don't look right, you can format storage and try again.
Please note that for Animal Crossing, subfolders are created. Each folder can contain only up to 100 files and there is a total of 400+ of Animal Crossing ones.