How to dump the Config Savegame
By default, Citra creates a dummy config file representing a 3DS console's config savegame, which is sufficient to play most games without any work by the user or any files dumped from a real console. However, a dump of a real config savegame from a physical 3DS is required if an error similar to below is encountered while using Citra:
Service.CFG <Error> core/hle/service/cfg/cfg.cpp:GetConfigInfoBlock:197: Config block 0xB0001 with flags 2 and size 2048 was not found
This tutorial will cover how to dump the config savegame (alongside its system archives and the shared fonts) from a 3DS console, but note that this file is copyrighted and not allowed to be shared, so don't ask for it on the forum. If you do not own a 3DS to dump a config savegame from, you are out of luck.
threeSD
threeSD is a tool written to help import data from your 3DS for Citra more conveniently.
Refer to threeSD Quickstart Guide for importing your installed titles, updates, DLCs, save data, extra data, system files, etc. Note that you'll still need a hacked 3DS with GodMode9 to obtain your keys so that threeSD can decrypt the data on your SD card.
Diagram showing the correct location of the config savegame in Citra's User Directory.
"User Directory"
└── nand
└── data
└── 00000000000000000000000000000000
└── sysdata
└── 00010017
└── 00000000
└── config