it depends on how your servers you play on are configured. if they are configured properly they should download the custom mods into thier own folder. I have more than 4 custom maps in my main folder. having more than that is only a SERVER limitation.
its possible that you may have a corrupted iwd file. you may have to reinstall the game. also they have just released the 1.3 patch for cod2 as well.
Normally I don't plug my own server here, but sometimes its easier to troubleshoot with a known quanity.
This is the ip of our server: 126.96.36.199:28960
we have quite a bit of cod2 info related to our server. Stop by and play sometime. http://v4v.us/
please note that on your first connect to our server you will get to download our mods and custom maps. It will take you a few min. to get that done. also make sure your punkbuster is updated. (pbweb from punkbuster's website)