After searching and troubleshooting all over the internet, I have decided to seek help here (fingers crossed). I currently work at a company that is migrating from a server over to Office 365. Currently we have shared folders on a server that we can all access, edit etc and each of us has our own personal folders that we keep private (on the server). I know you can add files and folders into SharePoint and then sync them to your OneDrive however once I do this all my personal files and folders are then shared to SharePoint which means everyone can see them. Any way to stop this? Keep them separate? It would be nice to just click on the OneDrive icon on my Windows10 desktop and be able to access my personal folder and all the SharePoint files and folders that I and my employees can edit, delete etc. Anyone have an answer?
That's exactly what OneDrive is, your own Private folder. Your SharePoint sites are for "teams" or shared folder like document libraries, althou things can be made private but that's the idea. You have a OneDrive - Org folder you can sync which are your files, then the Sites - Org folder which is your SharePoint synced libraries.
So planning for that, you guys need to include OneDrive with the deployment to move those private folders too.