I got several PMs about this now: Clookie, plzzee tell me... How does this work...  

So: It's not difficult.

Load the game into the ROM Tool, click "ignore" (or whatever) when a window pops up, then you click the tab Export, select AP Patch and export the patched ROM.

That's it. It's that easy.

If someone would like to create an illustrated tutorial, than he should do that. But we have such smart users here at DS Scene, they patch their ROMs like a Pro!