Of course not. You should format the micro sd card to fat32 or even better exFat, since Fat32 will have problems with big roms. Other than this, it is just a copy and paste process... Just remember to always copy roms one at a time to avoid fragmentation errors, and never delete roms, just format the sd card and start from scratch.
Also, avoid placing Pokemon and Animal Crossing roms on the gateway, again to avoid fragmentation errors, since those save to the rom itself and could produce issues. If you can, install those as CIAs instead.
Now for the last steps to set-up your GW3DS to play 3DS ROMs. Assuming you have already downloaded the Win32 Disk Imager program, the next step is to navigate to your 3DS ROM collection. The 3DS ROMs have a file extension of .3DS. With the newest GW3DS update you can now flash any 3DS rom from any region onto the microSD card and have it play on any region 3DS system. With the microSD card plugged into your computer, start up the Win32 Disk Imager. This program is recommended to write the 3DS ROM to the microSD card. Once Win32 Disk Imager is loaded, be sure to check that your microSD card drive letter is selected, if it is not you may end up writing the ROM to another device.
That's the reason why Gateway should finally create a guide with all available info .... there is also shitloads of information spread all over the web, which will become a problem in the future if it's not found in one place.