Thanks. I got it.

You can either use criteria like Genre doesn't equal or Path doesn't equal or if you have no way to exclude by criteria create a Playlist of these files and then use the criteria Playlist doesn't equal.

When creating a collection, I don't see a way to exclude.

Create an Auto-Playlist or Collection that excludes these specific files and sync that. Auto-Playlists and Collections will auto-update on any changes made including removing/adding files to the Library.

Is there a way to simply exclude folders/artists/albums from sync? I'd like to have my entire library synced, including music I add later (without having to add these new subfolders to sync), but choose a few files/folder I never want to sync.