You place all the folders you want to sync in one master folder (only one level deep) and sync the master folder. Each subfolder will sync as an album with the same name as the folder.
To sync additional folders, place them in the master folder and sync again.
If you choose to sync selected albums/folder instead of All in the Photo sync settings in iTunes, you can choose what subfolders (in the master folder) to sync.
For your case, this means you can select the main PC folder you mentioned, then select all the subfolder you want to sync, provided they are only one level down.
However, I recommend creating a folder specifically for syncing with iOS and placing copies of folders and pictures in it. This way you can tune/add/delete the pictures you want without worrying about whether you've just deleted or misplaced the only copy you have.
iOS and iPod: Syncing photos using iTunes