By default Bitrix24 "My Drive" is synchronized with "Bitrix24" folder on your computer. If you need "Company Drive" files or\and folders to be synchronized as well, you will need to connect them to "My Drive" first: open Company Drive, choose file\folder and click option "Connect to Drive":
This file\folder will appear in "My Drive" and will be synchronized to your computer together will other "My Drive" files and folders.
Please note that you can always disconnect files\folders previously connected to "My Drive" from Company Drive or Workgroups. To do that - please open My Drive, choose file\folder, click "disconnect" in the file\folder's menu: