You can set the watch folder location by using the ADM client application.
Log into ADM Client as a user with access to System Control (usually your MSTR user)
Select System Control
Select Watched Folders under Document Processing
Select the relevant Watch Folder followed by Edit Watch Folder
Update or browse to the relevant Watched Folder Path
Select OK
For your scanners, you would need to refer this to your IT department as they will need to make the adjustments necessary to set the scanner to store your documents in the relevant location.