Just make a folder called 'Data' or whatever, and put inside your edited folders and files (respecting the game data structure).
e.g:
Data\
Monster\Monster.SData
Monster\NpcSkill.SData
Then use
[Only registered and activated users can see links. Click Here To Register...] to create a Patch, it will ask you for the patch number.
-In the Tool, select File > New > Patch
-Choose the folder where you will Save the new created patch.
-Click the
Import Folder icon (upper right corner) and choose the
folder where you put your edited files ('Data' in the example).
It will import your files, check that everything is ok (structure, etc)
Click the
Save Patch icon, and thats all.
You can also use this tool to apply the patch to your client.