I found these 2 links very helpful and informative which explain how to use PowerShell commands to observe the current setting of Windows Defender and make configuration changes such as disabling and enabling, and how to add exclusions on certain apps.
and this one, which has a short but helpful video: http://www.netometer.com/blog/?p=1579
Add Windows Defender exclusion for iBackup exe
In my case, I wanted to add an exclusion for the iBackup exe which runs nightly to do a local disk backup to another drive on the same machine, and Windows Defender was watching every file write operation in real time, and this made the backup take a very long time. So, I added an exclusion for the iBackup processes exe using this command, and it sped up the backup tremendously:
Set-MpPreference -ExclusionProcess "C:\Program Files (x86)\IBackupWindows\cmd_util\ibwutil_100.exe"