Unless these template folders are Subfolder under a higher level folder synchronize won't add them. you have to import them.
LR is not a File browser. It only knows folders you have imported images from. In the Import dialog you can select multiple folders to import images from. Just hold down the Ctrl (Windows) or Command (Mac) key and select the multiple folders you want to import images from.
The import dialog window is the only part of LR that sees all drives connected to your system and any networked drive you have access to on your LAN.