Inside the _SYSTEM_ directory there is the "theme" directory. Inside that are the themes folders (theme01, theme02 etc). You have to replace one of the 12 skins present with your new skin - open up one of the "theme0x" directories and copy your bmp files in there.
Be sure that you saved the images you created as a 24bit bitmap.
I downloaded the "DS menu offset" the from NDS Themes
And it only showed the lower screen image. Then I found out about the bitrate