For FTP, I use FTPD with FileZilla, but unless you got less than 4GBs or so worth of stuff and a good connection, it will take HOURS! Highly suggest using an SD card reader instead, as it's roughly 20 times faster, maybe even more (3DS wifi is bad so you won't ever get more than 1MB/s whereas with a card reader you can easily get 20MB/s).
After you backup all contents from the SD card, remember to delete from the SD card the NAND dumps and all that as the take like 2-3GBs total and aren't needed until you need to restore your 3DS to a previous state. Instead, keep those backups only on your PC and if you ever need them, then move them back to the SD card. Save backups though hardly take any space, so feel free to keep those on the SD card (got like 400 game saves backed up and only take like 80MBs).
PS: Also, yes, boot9/boot11 are the same thing as arm9/arm11 dumps.