Step 1. Format the MicroSDHC using the official SD Association format utility from
https://www.sdcard.o...ds/formatter_3/ -- The default settings are fine, I advise against doing "full" format unless you're troubleshooting corruption issues (because it will take a VERY long time on 4GB+ MicroSDHC).
Step 2. Download the "Newest Wood R4 Kernel" from
http://r4ids.cn/r4i-download-e.html
Step 2a. (Optional) Download
3DS V2.2.0-4 Patch Nov. 21, 2011 (Firmware Upgrade) from
http://r4ids.cn/r4i-download-e.html
Step 3. Extract both archives to a temporary folder you're preparing to copy to the MicroSD
It should look something like this, as the text files aren't needed on the memory card:
You can delete the Firmware Upgrade (.nds) files after successfully patching your cartridge directly within the Wood system menu.
(Side note: The reason there's two different versions for the firmware update happens to be because the DSi and 3DS don't permit live cartridge swaps when you run the homebrew used to flash the firmware.)
Step 3a. (Optional) Download a ROM trimming utility such as NDSTokyoTrim or TinyTrimmer from FileTrip to reduce the filesizes of your commercial ROMs without compressing them.
Step 4. Add whatever games, homebrew, etc, to the Wood directory. You can create subdirectories to organize them.
Step 5. Copy it all over to the MicroSD.
Put MicroSD in Cart, Load, Enjoy! If you decide to get custom skins, make sure they are Acekard format and not "R4 format" skins.
For future Wood kernel updates, you can simply update through the Wood menu under "Tools".
For future Firmware updates you will have to keep tabs on the
http://www.r4ids.cn website.