Yep don't forget to change the extention to .3dz after you've injected a header.
How do I inject a header?
is the extension changed to .3dz after the rom has been put on the sd card or before?
http://gbatemp.net/threads/how-to-use-scene-dumps-with-gw-2-2-online.365829/
Everything you need to know is on the first page there, that will show you how to inject headers etc. After It's done you rename the rom to .3dz yourself.
Tried to download the Rom patcher, I get the following 'the archive is either in unknown format or damaged'