First of all , I make sure iTunes doesn't 'Manage' my music. ie, it doesn't move it, copy it or do anything else to it. It's in the Preferences somewhere.
I then have a Folder that contains my bounced songs. I make a folder within that folder for each band or artist and their songs go in their allocated folder.
Open iTunes. Drag the wavs onto iTunes.
The songs all appear in the iTunes library but iTunes hasn't moved any of them. They are still physically in that folder I made and manage myself.
You can then make as many or as few playlists as you want containing any or all of your songs or a combination. I treat playlists for this purpose as temporary things.
If someone wants an AAC (which they rarely do, they are usually way happier with me WeTransferring the full quality wav) I can make endless AAC's or MP3's from my wavs in iTunes at different qualities (it's always set to the higest quality, but one has the choice), all from the full quality wav I have bounced.
But this is just how I do it. There are many ways and this has always worked ok for me although I now only have a few clients who want CD's. I still organise my finished or work in progress files this way though as it makes it easier for me to keep track and quickly supply files if people ask,