Hi,
As far as I know, Office365 with OneDrive for Business (formly SkyDrive Pro) will sync the whole library you selected from Office365 site by design, it's unable to sync the folder inside a library from SharePoint site.
A workaround in the mean time would be to split your files and folders in to separate document libraries and then sync only the libraries you need. You can add new libraries to your OneDrive for Business by clicking the cog icon top right then selecting
"Add an app".
As mentioned in a previous answer, drive mapping can work as an alternative too. This way your work with your files "live" and nothing gets downloaded only the files you work with. Look at
http://support.microsoft.com/en-us/kb/2616712 on how to map network drives and
http://www.lieben.nu/numb3rs/?page_id=129 and http://www.thinkscape.com/Map-Network-Drives-To-Office-365-OneDrive/
on how to automate the mapping process.
Please Note: Since the web site is not hosted by Microsoft, the link may change without notice. Microsoft does not guarantee the accuracy of this information.
Reference:
https://social.technet.microsoft.com/Forums/sharepoint/en-US/7f3e9994-9ca3-4550-b82e-2bfe64eab692/folder-selective-sync-with-onedrive-for-business?forum=sharepointgeneral
Regards,
George Zhao
Forum Support
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