When you set up a directory synchronization between a local active directory and Office 365, the sync runs immediately. After that, it runs automatically every three hours. However, there are many cases where you may want to do a manual dirsync of the directories immediately, especially while setting up and testing the system.
The first way to run an office 365 manual dirsync is to run the dirsync configuration again, just like you did to set it up initially. However, this is a bit of a pain as it requires re-entering all your admin usernames and passwords every time you want to just sync the directories. There is a much easier method.
Open windows explorer, and navigate to the following file. When open it, it will open a command prompt.
c:\program files\microsoft online directory sync\dirsyncconfigshell.psc1
Once the command prompt is open, run the command:
This will cause an immediate manual dirsync. This should get the directories syncing, and depending on a number of factors, it will likely only take a few minutes at the most (much less if the directories and changes are small). You should now go to the Office 365 admin portal and confirm whatever directory changes you made are synced up now.