Is there a way to move from flat to folder per season?

Currently my shows are mostly organized by season, but a big portion of them are flat. I'd like to convert them all to folders by season, and before I take on the task of doing it manually, I'd like to know:

Does TV Rename have a move & organize by folder or flat function built in to it?

Yes and no. There is a bit of manual work to do.

First you need to enable the season per folder option on each of your series that is currently flat. That means highlight each show (not the season) one by one and choose edit to change the show setting.

Second, do a missing check. TVRename will create all your season folders and tell you that all your shows are now missing.

Third - Add every folder that is the top level show folder into the search folders section of the Finding and renaming tab. Run the Find and you should find all your shows and want to move them a folder below - very quick move.

Of course you can try this on one or two shows to see what I mean, or do the job in batches, or do the whole lot at once, or move all you files to a temporary folder and just search in that folder. You can make it as easy as you like, but there is no built in function to do this.

First you need to enable the season per folder option on each of your series that is currently flat.
If you're happy editing the main settings file's XML with a text editor, you can search and replace on the "FolderPerSeason" tag and set it to "true". Don't forget to quit tvrename before editing!

Third - Add every folder that is the top level show folder into the search folders section of the Finding and renaming tab.
You can add your media server's root folder, so rather than d:\media\show1, d:\media\show2, etc.. just add "d:\media" to the search folders. Folders can be added to this list (and most other lists) by dragging+dropping the folder from explorer into the list area.

Also: When you're doing finding&organising, after doing the "Find" you can select rows in the list and hit "Del" on your keyboard to remove them. This will let you take out ones that look horribly wrong, so only what it left will be done when you click "Move/Copy". They'll come back next time you click "Find".