Finally OneDrive really is OneDrive, The next gen client uses the same engine for OneDrive personal and OneDrive for business. I have always found the OneDrive personal client better than the OneDrive for business client.
The next gen client uses the same engine and it just works, no more sync issues. To ensure you are using the correct client browse to https://onedrive.live.com/about/en-us/download/ and click on the download link and update your client.
After your client is updated you should have version 17.3.6381.0405 as per the image below
After the client has been updated, Sync your personal OneDrive and select only the folders required. Then right click on the OneDrive icon in the system tray and select : settings. You can now add a business account as per the image below and select only folders required for syncing.
If you have Office installed the next thing is to disable OneDrive for Business client startup which is part of the Office suite as per image below.
So now finally , OneDrive simply works and a lot of the old limitations like the 20,000 item sync limit have been removed.