Been a while since I've used itunes, I presume your itunes library is just a bunch of movies/tv episodes/music in different folders?
Shouldn't affect it at all, in fact there's probably some itunes features built in. The server bit is free, you can get all that set up very quickly. I think it does prefer files to be in separate folders though, so for 1 folder for movies, another for TV shows and so on, then each movie in its own folder within the parent folder, each tv show in their own folder etc. You can always manually match videos or music that plex doesn't automatically match as well. And of course you can change cover art to your liking.
All it does is read whats in the folders you choose to add to it, then downloads the info/cover art etc for them and adds them to your library. It doesn't change anything in your actual folders, the only thing it does do is add a cache where it stores all the information.
Edit: Looks like it may even automatically acquire itunes content, so you wouldn't even need to add the folders/files separately.
For example this is how my movies section within plex media server on windows looks: