All custom files have to be in zip files with the same file structure as the data folder. When you got a custom monster graphic, for example, you create a folder "graphics" in the zip, in that folder a folder "sprites" and you put the monster graphic in there.
Then you have to create a resources2.txt. This is a list of all files the client has to download followed by their adler32 checksums (Google for a tool to calculate those).
Then you could use a news.txt containing something for your players to read while they update.
Put al this into the same folder on your webserver and tell your users to set this as your update host.
This is how the update folder on the official server looks:
http://updates.themanaworld.org/