Your best bet is to prevent iTunes from managing your music files. You control where they're stored and their filesystem hierarchy and just let iTunes see and play them. Otherwise you may never be satisfied with the way iTunes keeps songs organized on disk.
So just put the MP3s files in the same hierarchy as your WMA files. you can leave them under the main folder they're in now and iTunes will continue to see them without any action. Or you can move them somewhere else and then toss them back into iTunes.
You can remove your WMA files and put them somewhere else for safe keeping. When iTunes no longer sees them you can use a tool to locate and remove them from its DB.
iTunify offers some tools you may find useful:
http://www.mistatree.org/Shareware/iTunify/I've now got all my music being managed by iTunes, but I keep my own file hierarchy. So I add tunes to the drive before letting iTunes see them.
I also keep all my music on an external volume which also holds the iTunes DB files. To do this you simply copy your iTunes folder to the other volume, make an alias of it, coy the alieas to where the folder is supposed to be and rename it to just "iTunes"
Something else you may find useful is accessing multiple databases with iTunes. If you hold down OPTION while starting it (SHIFT on Windows i believe) you will be prompted for an alternate DB location. Great way to keep multiple collections without intermingling them. They can overlap in tunes from disk of course if you're managing that yourself as mentioned above.
Bruno